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/7770667/working' mkdir: created directory `/scratch/stefan/7770667/working/protonate' Storing results in /scratch/stefan/7770667/finished Working in /scratch/stefan/7770667/working /scratch/stefan/7770667/working /scratch/stefan/7770667 /scratch/stefan/7770667/working/protonate /scratch/stefan/7770667/working /scratch/stefan/7770667 Precomputing protomers for all compounds (pH: 7.4) ph 7.4: 268 protomers created Coalesing and merging protomers 268 protomers generated for 134 compounds Checking for new stereocenters and expanding 268 protomers after new stereo-center expansion /scratch/stefan/7770667/working /scratch/stefan/7770667 Bulk generating 3D conformations all protomers in /scratch/stefan/7770667/working/3D mkdir: created directory `/scratch/stefan/7770667/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7770667/working/protonate/xaaaagz-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' 269 3D conformations generated for 134 compounds Building REAL300020312529 mkdir: created directory `/scratch/stefan/7770667/working/building' mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312529' /scratch/stefan/7770667/working/building/REAL300020312529 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312529 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312529/0 /scratch/stefan/7770667/working/building/REAL300020312529 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/1 `/scratch/stefan/7770667/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(C(=O)OC(C)(C)C)C1) `REAL300020312529.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312529 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 4, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 1, 1, 1, 1, 6, 6, 6, 6, 53, 53, 95, 97, 97, 97, 6, 9, 9, 9, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 97, 97, 97, 97, 97, 97, 97, 97, 97, 6, 6] 151 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 249 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312529 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 15, 6, 6, 6, 6, 10, 10, 12, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 1, 13, 13, 35, 38, 38, 38, 1, 26, 26, 26, 15, 15, 10, 10, 10, 10, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1] 151 rigid atoms, others: [51, 37, 38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 52, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 212 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312529 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 8, 5, 5, 4, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 12, 12, 12, 70, 70, 105, 107, 107, 107, 12, 13, 13, 13, 8, 8, 4, 4, 2, 2, 12, 12, 12, 12, 12, 107, 107, 107, 107, 107, 107, 107, 107, 107, 12, 12] 151 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 285 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312529 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312529/1 /scratch/stefan/7770667/working/building/REAL300020312529 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/2 `/scratch/stefan/7770667/working/3D/2' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(C(=O)OC(C)(C)C)C1) `REAL300020312529.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312529/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312529 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 4, 1, 1, 1, 1, 4, 4, 5, 5, 5, 5, 1, 1, 1, 1, 6, 6, 6, 6, 53, 53, 95, 97, 97, 97, 6, 9, 9, 9, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 97, 97, 97, 97, 97, 97, 97, 97, 97, 6, 6] 151 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 249 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312529 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [26, 26, 15, 6, 6, 6, 6, 10, 10, 12, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 1, 13, 13, 35, 38, 38, 38, 1, 26, 26, 26, 15, 15, 10, 10, 10, 10, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1] 151 rigid atoms, others: [51, 37, 38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 52, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 212 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312529 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 8, 5, 5, 4, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 12, 12, 12, 70, 70, 105, 107, 107, 107, 12, 13, 13, 13, 8, 8, 4, 4, 2, 2, 12, 12, 12, 12, 12, 107, 107, 107, 107, 107, 107, 107, 107, 107, 12, 12] 151 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 285 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312529 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312529 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `/scratch/stefan/7770667/finished' Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312529/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312529/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312529 Building REAL300020312530 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312530' /scratch/stefan/7770667/working/building/REAL300020312530 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312530 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312530/0 /scratch/stefan/7770667/working/building/REAL300020312530 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/3 `/scratch/stefan/7770667/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(C(=O)OC(C)(C)C)C1) `REAL300020312530.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312530 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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: [9, 9, 4, 1, 1, 1, 1, 2, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 5, 55, 55, 93, 95, 95, 95, 5, 9, 9, 9, 4, 4, 2, 2, 5, 5, 5, 5, 5, 95, 95, 95, 95, 95, 95, 95, 95, 95, 5, 5] 201 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312530 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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: [19, 19, 12, 5, 5, 5, 5, 8, 16, 16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 1, 13, 13, 29, 32, 32, 32, 1, 19, 19, 19, 12, 12, 8, 8, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1] 201 rigid atoms, others: [48, 34, 35, 36, 37, 38, 49, 14, 15, 16, 17, 18, 19, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 180 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312530 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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: [16, 16, 12, 4, 4, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 16, 16, 16, 16, 118, 118, 165, 166, 166, 166, 16, 16, 16, 16, 12, 12, 3, 3, 16, 16, 16, 16, 16, 166, 166, 166, 166, 166, 166, 166, 166, 166, 16, 16] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 416 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312530 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312530/1 /scratch/stefan/7770667/working/building/REAL300020312530 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/4 `/scratch/stefan/7770667/working/3D/4' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(C(=O)OC(C)(C)C)C1) `REAL300020312530.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312530 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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: [9, 9, 4, 1, 1, 1, 1, 2, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 5, 55, 55, 93, 95, 95, 95, 5, 9, 9, 9, 4, 4, 2, 2, 5, 5, 5, 5, 5, 95, 95, 95, 95, 95, 95, 95, 95, 95, 5, 5] 201 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312530 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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: [19, 19, 12, 5, 5, 5, 5, 8, 16, 16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 1, 13, 13, 29, 32, 32, 32, 1, 19, 19, 19, 12, 12, 8, 8, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1] 201 rigid atoms, others: [48, 34, 35, 36, 37, 38, 49, 14, 15, 16, 17, 18, 19, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 180 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312530 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(C(=O)OC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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: [16, 16, 12, 4, 4, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 16, 16, 16, 16, 120, 120, 168, 168, 168, 168, 16, 16, 16, 16, 12, 12, 3, 3, 16, 16, 16, 16, 16, 168, 168, 168, 168, 168, 168, 168, 168, 168, 16, 16] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 416 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312530 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312530 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312530/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312530/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312530 Building REAL300020312531 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312531' /scratch/stefan/7770667/working/building/REAL300020312531 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312531 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312531/0 /scratch/stefan/7770667/working/building/REAL300020312531 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/5 `/scratch/stefan/7770667/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC(C(=O)OC)OC(C)(C)C1) `REAL300020312531.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312531 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC(C(=O)OC)OC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 11, 12, 5, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 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: [10, 10, 5, 1, 1, 1, 1, 5, 9, 14, 14, 14, 14, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 4, 4, 4, 4, 4, 10, 10, 10, 5, 5, 5, 5, 9, 9, 4, 4, 4, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4] 182 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 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: 114 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312531 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC(C(=O)OC)OC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 11, 12, 5, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 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: [22, 22, 11, 4, 4, 4, 4, 16, 28, 37, 37, 37, 37, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 22, 22, 22, 11, 11, 16, 16, 28, 28, 1, 1, 1, 4, 4, 4, 2, 2, 2, 2, 2, 2, 1, 1] 182 rigid atoms, others: [49, 37, 38, 39, 50, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 253 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312531 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC(C(=O)OC)OC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 11, 12, 5, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 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: [45, 45, 33, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 38, 38, 38, 100, 100, 100, 38, 38, 38, 38, 38, 45, 45, 45, 33, 33, 6, 6, 4, 4, 38, 38, 38, 100, 100, 100, 38, 38, 38, 38, 38, 38, 38, 38] 182 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 414 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312531 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312531/1 /scratch/stefan/7770667/working/building/REAL300020312531 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/6 `/scratch/stefan/7770667/working/3D/6' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC(C(=O)OC)OC(C)(C)C1) `REAL300020312531.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312531 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC(C(=O)OC)OC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 11, 12, 5, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 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: [10, 10, 5, 1, 1, 1, 1, 5, 9, 14, 14, 14, 14, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 4, 4, 4, 4, 4, 10, 10, 10, 5, 5, 5, 5, 9, 9, 4, 4, 4, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4] 182 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 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: 114 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312531 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC(C(=O)OC)OC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 11, 12, 5, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 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: [22, 22, 11, 4, 4, 4, 4, 16, 28, 37, 37, 37, 37, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 22, 22, 22, 11, 11, 16, 16, 28, 28, 1, 1, 1, 4, 4, 4, 2, 2, 2, 2, 2, 2, 1, 1] 182 rigid atoms, others: [49, 37, 38, 39, 50, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 253 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312531 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC(C(=O)OC)OC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 11, 12, 5, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 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: [45, 45, 34, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 38, 38, 38, 100, 100, 100, 38, 38, 38, 38, 38, 45, 45, 45, 34, 34, 6, 6, 4, 4, 38, 38, 38, 100, 100, 100, 38, 38, 38, 38, 38, 38, 38, 38] 182 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 414 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312531 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312531 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312531/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312531/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312531 Building REAL300020312532 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312532' /scratch/stefan/7770667/working/building/REAL300020312532 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312532 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312532/0 /scratch/stefan/7770667/working/building/REAL300020312532 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/7 `/scratch/stefan/7770667/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC(C(=O)OC)OC(C)(C)C1) `REAL300020312532.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312532 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC(C(=O)OC)OC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 11, 12, 5, 12, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 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: [10, 10, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 4, 4, 4, 4, 4, 10, 10, 10, 5, 5, 6, 6, 4, 4, 4, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4] 127 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 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: 87 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312532 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC(C(=O)OC)OC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 11, 12, 5, 12, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 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: [20, 20, 11, 4, 4, 4, 4, 15, 21, 21, 21, 21, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 20, 20, 20, 11, 11, 15, 15, 1, 1, 1, 4, 4, 4, 2, 2, 2, 2, 2, 2, 1, 1] 127 rigid atoms, others: [34, 35, 36, 14, 15, 16, 17, 18, 46, 22, 23, 24, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 160 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312532 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC(C(=O)OC)OC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 11, 12, 5, 12, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 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: [23, 23, 18, 6, 6, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 19, 19, 19, 51, 51, 51, 19, 19, 19, 19, 19, 23, 23, 23, 18, 18, 3, 3, 19, 19, 19, 51, 51, 51, 19, 19, 19, 19, 19, 19, 19, 19] 95 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 210 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312532 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312532/1 /scratch/stefan/7770667/working/building/REAL300020312532 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/8 `/scratch/stefan/7770667/working/3D/8' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC(C(=O)OC)OC(C)(C)C1) `REAL300020312532.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312532/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312532 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC(C(=O)OC)OC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 11, 12, 5, 12, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 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: [10, 10, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 4, 4, 4, 4, 4, 10, 10, 10, 5, 5, 6, 6, 4, 4, 4, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4] 127 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 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: 87 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312532 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC(C(=O)OC)OC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 11, 12, 5, 12, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 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: [20, 20, 11, 4, 4, 4, 4, 15, 21, 21, 21, 21, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 1, 20, 20, 20, 11, 11, 15, 15, 1, 1, 1, 4, 4, 4, 2, 2, 2, 2, 2, 2, 1, 1] 127 rigid atoms, others: [34, 35, 36, 14, 15, 16, 17, 18, 46, 22, 23, 24, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 160 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312532 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC(C(=O)OC)OC(C)(C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 11, 12, 5, 12, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 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: [23, 23, 18, 6, 6, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 19, 19, 19, 51, 51, 51, 19, 19, 19, 19, 19, 23, 23, 23, 18, 18, 3, 3, 19, 19, 19, 51, 51, 51, 19, 19, 19, 19, 19, 19, 19, 19] 95 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 210 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312532 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312532 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312532/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312532/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312532 Building REAL300020312533 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312533' /scratch/stefan/7770667/working/building/REAL300020312533 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312533 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312533/0 /scratch/stefan/7770667/working/building/REAL300020312533 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/9 `/scratch/stefan/7770667/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(C(=O)OC)(C(F)F)CC1) `REAL300020312533.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312533 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(C(=O)OC)(C(F)F)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 15, 15, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 4, 6, 6, 6, 6, 1, 1, 1, 1, 5, 5, 5, 5, 15, 15, 15, 5, 16, 16, 5, 5, 11, 11, 11, 5, 5, 4, 4, 5, 5, 5, 5, 15, 15, 15, 16, 5, 5, 5, 5] 177 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 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: 140 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312533 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(C(=O)OC)(C(F)F)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 15, 15, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 12, 5, 5, 5, 5, 10, 16, 16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 6, 6, 1, 1, 20, 20, 20, 12, 12, 10, 10, 1, 1, 1, 1, 5, 5, 5, 6, 1, 1, 1, 1] 177 rigid atoms, others: [35, 36, 37, 38, 43, 44, 45, 14, 15, 16, 17, 18, 19, 46, 23, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 24, 25, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42]) total number of confs: 142 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312533 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(C(=O)OC)(C(F)F)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 15, 15, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 19, 6, 6, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 16, 16, 16, 16, 55, 55, 55, 16, 49, 49, 16, 16, 31, 31, 31, 19, 19, 3, 3, 16, 16, 16, 16, 55, 55, 55, 49, 16, 16, 16, 16] 176 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 397 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312533 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312533/1 /scratch/stefan/7770667/working/building/REAL300020312533 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/10 `/scratch/stefan/7770667/working/3D/10' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(C(=O)OC)(C(F)F)CC1) `REAL300020312533.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312533 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(C(=O)OC)(C(F)F)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 15, 15, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 4, 6, 6, 6, 6, 1, 1, 1, 1, 5, 5, 5, 5, 15, 15, 15, 5, 16, 16, 5, 5, 11, 11, 11, 5, 5, 4, 4, 5, 5, 5, 5, 15, 15, 15, 16, 5, 5, 5, 5] 176 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 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: 140 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312533 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(C(=O)OC)(C(F)F)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 15, 15, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 12, 5, 5, 5, 5, 10, 16, 16, 16, 16, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 6, 6, 1, 1, 20, 20, 20, 12, 12, 10, 10, 1, 1, 1, 1, 5, 5, 5, 6, 1, 1, 1, 1] 176 rigid atoms, others: [35, 36, 37, 38, 43, 44, 45, 14, 15, 16, 17, 18, 19, 46, 23, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 24, 25, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42]) total number of confs: 142 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312533 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(C(=O)OC)(C(F)F)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 15, 15, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 19, 6, 6, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 16, 16, 16, 16, 55, 55, 55, 16, 49, 49, 16, 16, 31, 31, 31, 19, 19, 3, 3, 16, 16, 16, 16, 55, 55, 55, 49, 16, 16, 16, 16] 176 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 397 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312533 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312533 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312533/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312533/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312533 Building REAL300020312534 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312534' /scratch/stefan/7770667/working/building/REAL300020312534 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312534 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312534/0 /scratch/stefan/7770667/working/building/REAL300020312534 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/11 `/scratch/stefan/7770667/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC[C@@H]1C) `REAL300020312534.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312534 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 10, 5, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 10, 10, 10, 5, 5, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5] 58 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 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: 101 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312534 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 15, 10, 5, 5, 5, 5, 17, 23, 39, 39, 39, 39, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 10, 10, 17, 17, 23, 23, 1, 1, 1, 1, 1, 1, 2, 2, 2] 58 rigid atoms, others: [32, 33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40]) total number of confs: 182 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312534 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 26, 16, 16, 8, 4, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 25, 25, 25, 25, 25, 25, 30, 30, 30, 26, 26, 8, 8, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25] 30 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312534 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312534/1 /scratch/stefan/7770667/working/building/REAL300020312534 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/12 `/scratch/stefan/7770667/working/3D/12' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC[C@@H]1C) `REAL300020312534.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312534 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 10, 5, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 10, 10, 10, 5, 5, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5] 58 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 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: 101 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312534 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 15, 10, 5, 5, 5, 5, 17, 23, 39, 39, 39, 39, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 10, 10, 17, 17, 23, 23, 1, 1, 1, 1, 1, 1, 2, 2, 2] 58 rigid atoms, others: [32, 33, 34, 35, 36, 37, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40]) total number of confs: 182 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312534 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 26, 16, 16, 8, 4, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 25, 25, 25, 25, 25, 25, 30, 30, 30, 26, 26, 8, 8, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25] 30 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312534 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312534 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312534/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312534/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312534 Building REAL300020312535 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312535' /scratch/stefan/7770667/working/building/REAL300020312535 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312535 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312535/0 /scratch/stefan/7770667/working/building/REAL300020312535 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/13 `/scratch/stefan/7770667/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CCC[C@@H]1C) `REAL300020312535.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312535 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 5, 5, 5, 5, 11, 11, 5, 5, 12, 12, 12, 12, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2] 20 rigid atoms, others: [36, 37, 38, 39, 40, 41, 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, 42, 43, 44]) total number of confs: 104 number of broken/clashed sets: 5 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312535 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 1, 1, 1, 1, 6, 6, 1, 1, 9, 9, 9, 9, 6, 6, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 13, 13, 13, 7, 7, 6, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5] 20 rigid atoms, others: [3, 4, 5, 6, 17, 18, 19, 20] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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: 82 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312535 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 17, 9, 9, 2, 2, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 20, 20, 20, 17, 17, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12] 20 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 79 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312535 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 14, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 20, 20, 20, 14, 14, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11] 20 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 15, 16] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 83 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312535 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312535/1 /scratch/stefan/7770667/working/building/REAL300020312535 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/14 `/scratch/stefan/7770667/working/3D/14' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CCC[C@@H]1C) `REAL300020312535.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312535/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312535 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 5, 5, 5, 5, 11, 11, 5, 6, 12, 12, 12, 12, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2] 20 rigid atoms, others: [36, 37, 38, 39, 40, 41, 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, 42, 43, 44]) total number of confs: 104 number of broken/clashed sets: 5 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312535 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 1, 1, 1, 1, 6, 6, 1, 1, 9, 9, 9, 9, 6, 6, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 13, 13, 13, 7, 7, 6, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5] 20 rigid atoms, others: [3, 4, 5, 6, 17, 18, 19, 20] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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: 82 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312535 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 17, 9, 9, 2, 2, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 20, 20, 20, 17, 17, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12] 20 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 71 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312535 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CCC[C@@H]1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 7, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 14, 6, 6, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 20, 20, 20, 14, 14, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11] 20 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 15, 16] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 83 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312535 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312535 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312535/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312535/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312535 Building REAL300020312536 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312536' /scratch/stefan/7770667/working/building/REAL300020312536 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312536 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312536/0 /scratch/stefan/7770667/working/building/REAL300020312536 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/15 `/scratch/stefan/7770667/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(CCC)CC1=CC(F)=CC=C1F) `REAL300020312536.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312536 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(CCC)CC1=CC(F)=CC=C1F NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 1, 1, 15, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 8, 5, 1, 1, 1, 1, 4, 6, 6, 6, 6, 1, 1, 1, 1, 4, 11, 14, 4, 13, 43, 43, 43, 43, 43, 43, 43, 8, 8, 8, 5, 5, 4, 4, 11, 11, 16, 16, 16, 16, 16, 13, 13, 43, 43, 43] 183 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 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: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312536 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(CCC)CC1=CC(F)=CC=C1F NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 1, 1, 15, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [82, 82, 70, 43, 43, 43, 43, 88, 102, 102, 102, 102, 43, 43, 24, 8, 24, 45, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 70, 70, 88, 88, 45, 45, 52, 52, 52, 52, 52, 8, 8, 1, 1, 1] 183 rigid atoms, others: [44, 45, 46, 19, 20, 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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312536 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(CCC)CC1=CC(F)=CC=C1F NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 1, 1, 15, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 17, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 16, 33, 39, 16, 39, 102, 102, 102, 102, 102, 102, 102, 20, 20, 20, 17, 17, 3, 3, 33, 33, 42, 42, 42, 42, 42, 39, 39, 102, 102, 102] 183 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 443 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312536 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312536/1 /scratch/stefan/7770667/working/building/REAL300020312536 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/16 `/scratch/stefan/7770667/working/3D/16' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(CCC)CC1=CC(F)=CC=C1F) `REAL300020312536.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312536/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312536 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(CCC)CC1=CC(F)=CC=C1F NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 1, 1, 15, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 8, 5, 1, 1, 1, 1, 4, 6, 6, 6, 6, 1, 1, 1, 1, 4, 11, 14, 4, 13, 43, 43, 43, 43, 43, 43, 43, 8, 8, 8, 5, 5, 4, 4, 11, 11, 16, 16, 16, 16, 16, 13, 13, 43, 43, 43] 185 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 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: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312536 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(CCC)CC1=CC(F)=CC=C1F NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 1, 1, 15, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [82, 82, 70, 43, 43, 43, 43, 88, 103, 103, 103, 103, 43, 43, 24, 8, 24, 45, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 70, 70, 88, 88, 45, 45, 52, 52, 52, 52, 52, 8, 8, 1, 1, 1] 185 rigid atoms, others: [44, 45, 46, 19, 20, 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, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312536 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(CCC)CC1=CC(F)=CC=C1F NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 1, 1, 15, 1, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 19, 16, 6, 6, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 16, 33, 39, 16, 40, 103, 103, 103, 103, 103, 103, 103, 19, 19, 19, 16, 16, 3, 3, 33, 33, 42, 42, 42, 42, 42, 40, 40, 103, 103, 103] 185 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 446 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312536 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312536 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312536/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312536/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312536 Building REAL300020312537 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312537' /scratch/stefan/7770667/working/building/REAL300020312537 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312537 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312537/0 /scratch/stefan/7770667/working/building/REAL300020312537 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/17 `/scratch/stefan/7770667/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC2(CCC2)CC(F)(F)C1) `REAL300020312537.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312537 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC2(CCC2)CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 15, 15, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 5, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 5, 5, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 64 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 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: 101 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312537 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC2(CCC2)CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 15, 15, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 12, 5, 5, 5, 5, 17, 26, 39, 39, 39, 39, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 12, 12, 17, 17, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 64 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 224 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312537 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC2(CCC2)CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 15, 15, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 26, 24, 14, 14, 8, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 26, 26, 26, 24, 24, 8, 8, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 29 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 125 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312537 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312537/1 /scratch/stefan/7770667/working/building/REAL300020312537 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/18 `/scratch/stefan/7770667/working/3D/18' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC2(CCC2)CC(F)(F)C1) `REAL300020312537.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312537/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312537 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC2(CCC2)CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 15, 15, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 5, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 5, 5, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 64 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 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: 101 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312537 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC2(CCC2)CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 15, 15, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 12, 5, 5, 5, 5, 17, 26, 39, 39, 39, 39, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 12, 12, 17, 17, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 64 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 224 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312537 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC2(CCC2)CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 15, 15, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 27, 24, 14, 14, 8, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 27, 27, 27, 24, 24, 8, 8, 4, 4, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 30 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 133 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312537 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312537 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312537/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312537/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312537 Building REAL300020312538 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312538' /scratch/stefan/7770667/working/building/REAL300020312538 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312538 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312538/0 /scratch/stefan/7770667/working/building/REAL300020312538 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/19 `/scratch/stefan/7770667/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC2(CCC2)CC(F)(F)C1) `REAL300020312538.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312538 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC2(CCC2)CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 35 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 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: 66 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312538 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC2(CCC2)CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 11, 4, 4, 4, 4, 12, 18, 18, 18, 18, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 11, 11, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 35 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 113 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312538 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC2(CCC2)CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 22, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 31, 31, 31, 22, 22, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 35 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 146 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312538 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312538/1 /scratch/stefan/7770667/working/building/REAL300020312538 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/20 `/scratch/stefan/7770667/working/3D/20' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC2(CCC2)CC(F)(F)C1) `REAL300020312538.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312538 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC2(CCC2)CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 35 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 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: 66 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312538 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC2(CCC2)CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 11, 4, 4, 4, 4, 12, 18, 18, 18, 18, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 11, 11, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 35 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 113 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312538 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC2(CCC2)CC(F)(F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 22, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 31, 31, 31, 22, 22, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 35 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 146 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312538 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312538 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312538/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312538/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312538 Building REAL300020312539 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312539' /scratch/stefan/7770667/working/building/REAL300020312539 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312539 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312539/0 /scratch/stefan/7770667/working/building/REAL300020312539 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/21 `/scratch/stefan/7770667/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(P(C)(C)=O)CC1) `REAL300020312539.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312539 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(P(C)(C)=O)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'P.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 13, 5, 5, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 5, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 4, 4, 4, 4, 24, 24, 24, 4, 4, 8, 8, 8, 5, 5, 5, 5, 9, 9, 4, 4, 4, 4, 4, 24, 24, 24, 24, 24, 24, 4, 4, 4, 4] 85 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 160 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312539 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(P(C)(C)=O)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'P.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 13, 5, 5, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 11, 4, 4, 4, 4, 16, 23, 36, 36, 36, 36, 4, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 1, 1, 12, 12, 12, 11, 11, 16, 16, 23, 23, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1] 85 rigid atoms, others: [48, 35, 36, 37, 38, 39, 46, 15, 16, 17, 18, 19, 20, 24, 25, 49, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45]) total number of confs: 184 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312539 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(P(C)(C)=O)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'P.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 13, 5, 5, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 30, 18, 18, 8, 4, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 38, 38, 38, 38, 74, 74, 74, 38, 38, 33, 33, 33, 30, 30, 8, 8, 4, 4, 38, 38, 38, 38, 38, 74, 74, 74, 74, 74, 74, 38, 38, 38, 38] 85 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 345 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312539 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312539/1 /scratch/stefan/7770667/working/building/REAL300020312539 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/22 `/scratch/stefan/7770667/working/3D/22' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(P(C)(C)=O)CC1) `REAL300020312539.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312539 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(P(C)(C)=O)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'P.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 13, 5, 5, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 5, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 4, 4, 4, 4, 23, 23, 23, 4, 4, 8, 8, 8, 5, 5, 5, 5, 9, 9, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 23, 4, 4, 4, 4] 85 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 157 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312539 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(P(C)(C)=O)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'P.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 13, 5, 5, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 11, 4, 4, 4, 4, 16, 23, 36, 36, 36, 36, 4, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 1, 1, 12, 12, 12, 11, 11, 16, 16, 23, 23, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1] 85 rigid atoms, others: [48, 35, 36, 37, 38, 39, 46, 15, 16, 17, 18, 19, 20, 24, 25, 49, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45]) total number of confs: 184 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312539 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(P(C)(C)=O)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'P.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 13, 5, 5, 11, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 30, 18, 18, 8, 4, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 37, 37, 37, 37, 74, 74, 74, 37, 37, 33, 33, 33, 30, 30, 8, 8, 4, 4, 37, 37, 37, 37, 37, 74, 74, 74, 74, 74, 74, 37, 37, 37, 37] 85 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 350 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312539 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312539 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312539/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312539/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312539 Building REAL300020312540 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312540' /scratch/stefan/7770667/working/building/REAL300020312540 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312540 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312540/0 /scratch/stefan/7770667/working/building/REAL300020312540 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/23 `/scratch/stefan/7770667/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(P(C)(C)=O)CC1) `REAL300020312540.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312540 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(P(C)(C)=O)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'P.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 13, 5, 5, 11, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 6, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 5, 5, 5, 5, 25, 25, 25, 5, 5, 12, 12, 12, 6, 6, 6, 6, 5, 5, 5, 5, 5, 25, 25, 25, 25, 25, 25, 5, 5, 5, 5] 102 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 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: 148 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312540 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(P(C)(C)=O)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'P.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 13, 5, 5, 11, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 13, 5, 5, 5, 5, 16, 22, 22, 22, 22, 5, 5, 1, 1, 1, 1, 1, 1, 10, 10, 10, 1, 1, 20, 20, 20, 13, 13, 16, 16, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1] 102 rigid atoms, others: [32, 33, 34, 35, 36, 43, 44, 45, 14, 15, 16, 17, 18, 19, 46, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42]) total number of confs: 159 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312540 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(P(C)(C)=O)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'P.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 13, 5, 5, 11, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 24, 8, 8, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 22, 22, 22, 22, 67, 67, 67, 22, 22, 38, 38, 38, 24, 24, 3, 3, 22, 22, 22, 22, 22, 67, 67, 67, 67, 67, 67, 22, 22, 22, 22] 102 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 366 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312540 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312540/1 /scratch/stefan/7770667/working/building/REAL300020312540 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/24 `/scratch/stefan/7770667/working/3D/24' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(P(C)(C)=O)CC1) `REAL300020312540.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312540/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312540 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(P(C)(C)=O)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'P.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 13, 5, 5, 11, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 6, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 5, 5, 5, 5, 25, 25, 25, 5, 5, 12, 12, 12, 6, 6, 6, 6, 5, 5, 5, 5, 5, 25, 25, 25, 25, 25, 25, 5, 5, 5, 5] 102 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 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: 148 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312540 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(P(C)(C)=O)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'P.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 13, 5, 5, 11, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 13, 5, 5, 5, 5, 16, 22, 22, 22, 22, 5, 5, 1, 1, 1, 1, 1, 1, 10, 10, 10, 1, 1, 20, 20, 20, 13, 13, 16, 16, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1] 102 rigid atoms, others: [32, 33, 34, 35, 36, 43, 44, 45, 14, 15, 16, 17, 18, 19, 46, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42]) total number of confs: 159 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312540 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(P(C)(C)=O)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'P.3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 13, 5, 5, 11, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [39, 39, 25, 8, 8, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 22, 22, 22, 22, 67, 67, 67, 22, 22, 39, 39, 39, 25, 25, 3, 3, 22, 22, 22, 22, 22, 67, 67, 67, 67, 67, 67, 22, 22, 22, 22] 102 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 369 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312540 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312540 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312540/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312540/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312540 Building REAL300020312541 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312541' /scratch/stefan/7770667/working/building/REAL300020312541 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312541 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312541/0 /scratch/stefan/7770667/working/building/REAL300020312541 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/25 `/scratch/stefan/7770667/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC2CC(C1)C(C(=O)OC)C2) `REAL300020312541.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312541 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC2CC(C1)C(C(=O)OC)C2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 5, 6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 9 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 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: 34 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312541 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC2CC(C1)C(C(=O)OC)C2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 3, 3, 3, 7, 8, 8, 8, 8, 8, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 4, 4, 4, 4, 4, 7, 7, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1] 9 rigid atoms, others: [50, 37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 16, 17, 18, 19, 20, 21, 22, 23, 49, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 35 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312541 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC2CC(C1)C(C(=O)OC)C2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 4, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 6 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 19 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312541 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312541/1 /scratch/stefan/7770667/working/building/REAL300020312541 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/26 `/scratch/stefan/7770667/working/3D/26' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC2CC(C1)C(C(=O)OC)C2) `REAL300020312541.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312541 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC2CC(C1)C(C(=O)OC)C2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 5, 6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 9 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 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: 34 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312541 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC2CC(C1)C(C(=O)OC)C2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 3, 3, 3, 7, 8, 8, 8, 8, 8, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 4, 4, 4, 4, 4, 7, 7, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1] 9 rigid atoms, others: [50, 37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 16, 17, 18, 19, 20, 21, 22, 23, 49, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 35 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312541 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC2CC(C1)C(C(=O)OC)C2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 4, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 6 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 19 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312541 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312541 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312541/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312541/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312541 Building REAL300020312542 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312542' /scratch/stefan/7770667/working/building/REAL300020312542 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312542 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312542/0 /scratch/stefan/7770667/working/building/REAL300020312542 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/27 `/scratch/stefan/7770667/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC2CC(C1)C(C(=O)OC)C2) `REAL300020312542.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312542 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC2CC(C1)C(C(=O)OC)C2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 3, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 3, 3, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 9 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 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: 40 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312542 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC2CC(C1)C(C(=O)OC)C2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 3, 2, 2, 2, 2, 6, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 4, 4, 4, 3, 3, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1] 9 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 46, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45]) total number of confs: 38 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312542 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC2CC(C1)C(C(=O)OC)C2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 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, 5, 5, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 5, 5, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 6 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 19 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312542 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312542/1 /scratch/stefan/7770667/working/building/REAL300020312542 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/28 `/scratch/stefan/7770667/working/3D/28' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC2CC(C1)C(C(=O)OC)C2) `REAL300020312542.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312542/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312542 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC2CC(C1)C(C(=O)OC)C2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 3, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 3, 3, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 9 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 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: 40 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312542 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC2CC(C1)C(C(=O)OC)C2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 3, 2, 2, 2, 2, 6, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 4, 4, 4, 3, 3, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1] 9 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 46, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45]) total number of confs: 38 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312542 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC2CC(C1)C(C(=O)OC)C2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 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, 5, 5, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 5, 5, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 6 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 19 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312542 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312542 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312542/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312542/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312542 Building REAL300020312543 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312543' /scratch/stefan/7770667/working/building/REAL300020312543 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312543 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312543/0 /scratch/stefan/7770667/working/building/REAL300020312543 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/29 `/scratch/stefan/7770667/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(COC(C)(C)C)CC1) `REAL300020312543.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312543 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(COC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 5, 9, 14, 14, 14, 14, 1, 1, 1, 1, 4, 4, 4, 4, 26, 51, 63, 63, 63, 4, 4, 11, 11, 11, 5, 5, 5, 5, 9, 9, 4, 4, 4, 4, 4, 26, 26, 63, 63, 63, 63, 63, 63, 63, 63, 63, 4, 4, 4, 4] 201 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 291 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312543 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(COC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 4, 4, 4, 4, 16, 22, 36, 36, 36, 36, 4, 4, 1, 1, 1, 1, 1, 1, 10, 26, 34, 34, 34, 1, 1, 20, 20, 20, 11, 11, 16, 16, 22, 22, 1, 1, 1, 1, 1, 10, 10, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 53, 54, 55, 56, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 295 number of broken/clashed sets: 48 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312543 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(COC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 18, 18, 6, 4, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 39, 39, 39, 39, 133, 155, 160, 160, 160, 39, 39, 61, 63, 63, 46, 46, 6, 6, 4, 4, 39, 39, 39, 39, 39, 133, 133, 160, 160, 160, 160, 160, 160, 160, 160, 160, 39, 39, 39, 39] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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, 54, 55, 56]) total number of confs: 759 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312543 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312543/1 /scratch/stefan/7770667/working/building/REAL300020312543 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/30 `/scratch/stefan/7770667/working/3D/30' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(COC(C)(C)C)CC1) `REAL300020312543.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312543/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312543 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(COC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 5, 9, 14, 14, 14, 14, 1, 1, 1, 1, 4, 4, 4, 4, 26, 53, 64, 64, 64, 4, 4, 11, 11, 11, 5, 5, 5, 5, 9, 9, 4, 4, 4, 4, 4, 26, 26, 64, 64, 64, 64, 64, 64, 64, 64, 64, 4, 4, 4, 4] 201 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 285 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312543 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(COC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 4, 4, 4, 4, 16, 22, 37, 37, 37, 37, 4, 4, 1, 1, 1, 1, 1, 1, 10, 28, 36, 36, 36, 1, 1, 20, 20, 20, 11, 11, 16, 16, 22, 22, 1, 1, 1, 1, 1, 10, 10, 36, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 53, 54, 55, 56, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 299 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312543 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(COC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 17, 17, 6, 4, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 40, 40, 40, 40, 130, 154, 157, 157, 157, 40, 40, 61, 62, 62, 45, 45, 6, 6, 4, 4, 40, 40, 40, 40, 40, 130, 130, 157, 157, 157, 157, 157, 157, 157, 157, 157, 40, 40, 40, 40] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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, 54, 55, 56]) total number of confs: 736 number of broken/clashed sets: 46 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312543 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312543 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312543/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312543/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312543 Building REAL300020312544 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312544' /scratch/stefan/7770667/working/building/REAL300020312544 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312544 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312544/0 /scratch/stefan/7770667/working/building/REAL300020312544 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/31 `/scratch/stefan/7770667/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(COC(C)(C)C)CC1) `REAL300020312544.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312544 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(COC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 4, 27, 55, 62, 62, 62, 4, 4, 11, 11, 11, 5, 5, 6, 6, 4, 4, 4, 4, 4, 27, 27, 62, 62, 62, 62, 62, 62, 62, 62, 62, 4, 4, 4, 4] 164 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 240 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312544 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(COC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 11, 4, 4, 4, 4, 15, 21, 21, 21, 21, 4, 4, 1, 1, 1, 1, 1, 1, 10, 26, 34, 34, 34, 1, 1, 21, 21, 21, 11, 11, 15, 15, 1, 1, 1, 1, 1, 10, 10, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1] 164 rigid atoms, others: [51, 34, 35, 36, 37, 38, 50, 14, 15, 16, 17, 18, 19, 52, 53, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 246 number of broken/clashed sets: 27 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312544 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(COC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [37, 37, 23, 8, 8, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 21, 21, 21, 21, 94, 122, 124, 124, 124, 21, 21, 37, 37, 37, 23, 23, 3, 3, 21, 21, 21, 21, 21, 94, 94, 124, 124, 124, 124, 124, 124, 124, 124, 124, 21, 21, 21, 21] 165 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 518 number of broken/clashed sets: 27 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312544 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312544/1 /scratch/stefan/7770667/working/building/REAL300020312544 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/32 `/scratch/stefan/7770667/working/3D/32' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(COC(C)(C)C)CC1) `REAL300020312544.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312544/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312544 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(COC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 4, 27, 56, 63, 63, 63, 4, 4, 11, 11, 11, 5, 5, 6, 6, 4, 4, 4, 4, 4, 27, 27, 63, 63, 63, 63, 63, 63, 63, 63, 63, 4, 4, 4, 4] 166 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 242 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312544 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(COC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 11, 4, 4, 4, 4, 15, 21, 21, 21, 21, 4, 4, 1, 1, 1, 1, 1, 1, 10, 26, 34, 34, 34, 1, 1, 21, 21, 21, 11, 11, 15, 15, 1, 1, 1, 1, 1, 10, 10, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1] 166 rigid atoms, others: [51, 34, 35, 36, 37, 38, 50, 14, 15, 16, 17, 18, 19, 52, 53, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 246 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312544 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(COC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 166 conformations in input total number of sets (complete confs): 166 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 23, 8, 8, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 21, 21, 21, 21, 95, 123, 125, 125, 125, 21, 21, 37, 37, 37, 23, 23, 3, 3, 21, 21, 21, 21, 21, 95, 95, 125, 125, 125, 125, 125, 125, 125, 125, 125, 21, 21, 21, 21] 166 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 521 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312544 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312544 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312544/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312544/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312544 Building REAL300020312545 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312545' /scratch/stefan/7770667/working/building/REAL300020312545 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312545 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312545/0 /scratch/stefan/7770667/working/building/REAL300020312545 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/33 `/scratch/stefan/7770667/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCCC(COC(C)(C)C)C1) `REAL300020312545.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312545 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCCC(COC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 5, 8, 13, 13, 13, 13, 1, 1, 1, 1, 5, 5, 5, 5, 5, 28, 55, 59, 59, 59, 5, 11, 11, 11, 5, 5, 5, 5, 8, 8, 5, 5, 5, 5, 5, 5, 5, 28, 28, 59, 59, 59, 59, 59, 59, 59, 59, 59, 5, 5] 201 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 243 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312545 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCCC(COC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 12, 5, 5, 5, 5, 17, 23, 38, 38, 38, 38, 5, 5, 1, 1, 1, 1, 1, 1, 1, 10, 23, 28, 28, 28, 1, 23, 23, 23, 12, 12, 17, 17, 23, 23, 1, 1, 1, 1, 1, 1, 1, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 55, 56, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 289 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312545 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCCC(COC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 41, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 40, 40, 40, 40, 40, 130, 148, 148, 148, 148, 40, 53, 53, 53, 41, 41, 6, 6, 4, 4, 40, 40, 40, 40, 40, 40, 40, 130, 130, 148, 148, 148, 148, 148, 148, 148, 148, 148, 40, 40] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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, 54, 55, 56]) total number of confs: 660 number of broken/clashed sets: 34 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312545 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312545/1 /scratch/stefan/7770667/working/building/REAL300020312545 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/34 `/scratch/stefan/7770667/working/3D/34' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCCC(COC(C)(C)C)C1) `REAL300020312545.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312545/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312545 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCCC(COC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 5, 8, 13, 13, 13, 13, 1, 1, 1, 1, 5, 5, 5, 5, 5, 28, 53, 57, 57, 57, 5, 11, 11, 11, 5, 5, 5, 5, 8, 8, 5, 5, 5, 5, 5, 5, 5, 28, 28, 57, 57, 57, 57, 57, 57, 57, 57, 57, 5, 5] 201 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 240 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312545 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCCC(COC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 12, 5, 5, 5, 5, 17, 23, 38, 38, 38, 38, 5, 5, 1, 1, 1, 1, 1, 1, 1, 10, 23, 28, 28, 28, 1, 23, 23, 23, 12, 12, 17, 17, 23, 23, 1, 1, 1, 1, 1, 1, 1, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 55, 56, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 289 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312545 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCCC(COC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens 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, 40, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 39, 39, 39, 39, 39, 131, 149, 149, 149, 149, 39, 53, 53, 53, 40, 40, 6, 6, 4, 4, 39, 39, 39, 39, 39, 39, 39, 131, 131, 149, 149, 149, 149, 149, 149, 149, 149, 149, 39, 39] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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, 54, 55, 56]) total number of confs: 674 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312545 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312545 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312545/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312545/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312545 Building REAL300020312546 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312546' /scratch/stefan/7770667/working/building/REAL300020312546 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312546 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312546/0 /scratch/stefan/7770667/working/building/REAL300020312546 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/35 `/scratch/stefan/7770667/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCCC(COC(C)(C)C)C1) `REAL300020312546.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312546 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCCC(COC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [11, 11, 5, 1, 1, 1, 1, 4, 6, 6, 6, 6, 1, 1, 1, 1, 5, 5, 5, 5, 5, 27, 46, 55, 55, 55, 5, 11, 11, 11, 5, 5, 4, 4, 5, 5, 5, 5, 5, 5, 5, 27, 27, 55, 55, 55, 55, 55, 55, 55, 55, 55, 5, 5] 149 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 234 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312546 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCCC(COC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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: [22, 22, 12, 5, 5, 5, 5, 13, 19, 19, 19, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 10, 20, 27, 27, 27, 1, 22, 22, 22, 12, 12, 13, 13, 1, 1, 1, 1, 1, 1, 1, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1] 149 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 53, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 224 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312546 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCCC(COC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 21, 6, 6, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 19, 19, 19, 19, 19, 76, 101, 104, 104, 104, 19, 33, 33, 33, 21, 21, 3, 3, 19, 19, 19, 19, 19, 19, 19, 76, 76, 104, 104, 104, 104, 104, 104, 104, 104, 104, 19, 19] 150 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 445 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312546 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312546/1 /scratch/stefan/7770667/working/building/REAL300020312546 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/36 `/scratch/stefan/7770667/working/3D/36' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCCC(COC(C)(C)C)C1) `REAL300020312546.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312546/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312546 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCCC(COC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 4, 6, 6, 6, 6, 1, 1, 1, 1, 5, 5, 5, 5, 5, 27, 46, 55, 55, 55, 5, 11, 11, 11, 5, 5, 4, 4, 5, 5, 5, 5, 5, 5, 5, 27, 27, 55, 55, 55, 55, 55, 55, 55, 55, 55, 5, 5] 150 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 234 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312546 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCCC(COC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 12, 5, 5, 5, 5, 13, 19, 19, 19, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 10, 20, 27, 27, 27, 1, 22, 22, 22, 12, 12, 13, 13, 1, 1, 1, 1, 1, 1, 1, 10, 10, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1] 150 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 53, 52, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 224 number of broken/clashed sets: 30 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312546 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCCC(COC(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 21, 6, 6, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 19, 19, 19, 19, 19, 76, 101, 104, 104, 104, 19, 33, 33, 33, 21, 21, 3, 3, 19, 19, 19, 19, 19, 19, 19, 76, 76, 104, 104, 104, 104, 104, 104, 104, 104, 104, 19, 19] 150 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 445 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312546 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312546 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312546/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312546/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312546 Building REAL300020312547 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312547' /scratch/stefan/7770667/working/building/REAL300020312547 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312547 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312547/0 /scratch/stefan/7770667/working/building/REAL300020312547 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/37 `/scratch/stefan/7770667/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCCC(P(C)(C)=O)C1) `REAL300020312547.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312547 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCCC(P(C)(C)=O)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'P.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 13, 5, 5, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 5, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 12, 5, 7, 7, 7, 5, 5, 3, 3, 4, 4, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 5, 5] 25 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312547 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCCC(P(C)(C)=O)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'P.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 13, 5, 5, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 9, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 1, 11, 11, 11, 9, 9, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1] 25 rigid atoms, others: [48, 35, 36, 37, 38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 25, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47]) total number of confs: 72 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312547 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCCC(P(C)(C)=O)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'P.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 13, 5, 5, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 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, 5, 5, 4, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 12, 12, 12, 7, 6, 6, 6, 6, 6, 4, 4, 2, 2, 7, 7, 7, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 7, 7] 15 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312547 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312547/1 /scratch/stefan/7770667/working/building/REAL300020312547 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/38 `/scratch/stefan/7770667/working/3D/38' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCCC(P(C)(C)=O)C1) `REAL300020312547.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312547/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312547 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCCC(P(C)(C)=O)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'P.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 13, 5, 5, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 5, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 12, 5, 7, 7, 7, 5, 5, 3, 3, 4, 4, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 5, 5] 26 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312547 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCCC(P(C)(C)=O)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'P.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 13, 5, 5, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 9, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 1, 11, 11, 11, 9, 9, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1] 26 rigid atoms, others: [48, 35, 36, 37, 38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 25, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312547 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCCC(P(C)(C)=O)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'P.3', 'C.3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 13, 5, 5, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 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, 5, 5, 4, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 12, 12, 12, 7, 6, 6, 6, 6, 6, 4, 4, 2, 2, 7, 7, 7, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 7, 7] 15 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312547 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312547 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312547/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312547/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312547 Building REAL300020312548 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312548' /scratch/stefan/7770667/working/building/REAL300020312548 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312548 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312548/0 /scratch/stefan/7770667/working/building/REAL300020312548 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/39 `/scratch/stefan/7770667/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCCC(P(C)(C)=O)C1) `REAL300020312548.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312548 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCCC(P(C)(C)=O)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'P.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 13, 5, 5, 11, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 5, 1, 1, 1, 1, 3, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 4, 4, 27, 27, 27, 4, 10, 10, 10, 5, 5, 3, 3, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 4, 4] 78 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 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: 138 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312548 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCCC(P(C)(C)=O)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'P.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 13, 5, 5, 11, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 11, 4, 4, 4, 4, 7, 13, 13, 13, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 1, 18, 18, 18, 11, 11, 7, 7, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 1, 1] 78 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 45, 14, 15, 16, 17, 18, 19, 20, 46, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44]) total number of confs: 134 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312548 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCCC(P(C)(C)=O)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'P.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 13, 5, 5, 11, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 15, 5, 5, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 13, 13, 13, 13, 58, 58, 58, 13, 20, 20, 20, 15, 15, 3, 3, 13, 13, 13, 13, 13, 13, 13, 58, 58, 58, 58, 58, 58, 13, 13] 78 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 265 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312548 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312548/1 /scratch/stefan/7770667/working/building/REAL300020312548 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/40 `/scratch/stefan/7770667/working/3D/40' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCCC(P(C)(C)=O)C1) `REAL300020312548.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312548 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCCC(P(C)(C)=O)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'P.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 13, 5, 5, 11, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 5, 1, 1, 1, 1, 3, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 4, 4, 27, 27, 27, 4, 10, 10, 10, 5, 5, 3, 3, 4, 4, 4, 4, 4, 4, 4, 27, 27, 27, 27, 27, 27, 4, 4] 78 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 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: 138 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312548 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCCC(P(C)(C)=O)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'P.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 13, 5, 5, 11, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 11, 4, 4, 4, 4, 7, 13, 13, 13, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 1, 18, 18, 18, 11, 11, 7, 7, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 1, 1] 78 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 45, 14, 15, 16, 17, 18, 19, 20, 46, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44]) total number of confs: 134 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312548 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCCC(P(C)(C)=O)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'P.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 13, 5, 5, 11, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 15, 5, 5, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 13, 13, 13, 13, 58, 58, 58, 13, 20, 20, 20, 15, 15, 3, 3, 13, 13, 13, 13, 13, 13, 13, 58, 58, 58, 58, 58, 58, 13, 13] 78 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 265 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312548 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312548 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312548/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312548/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312548 Building REAL300020312549 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312549' /scratch/stefan/7770667/working/building/REAL300020312549 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312549 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312549/0 /scratch/stefan/7770667/working/building/REAL300020312549 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/41 `/scratch/stefan/7770667/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC(=O)N2CCCCC2C1) `REAL300020312549.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312549 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC(=O)N2CCCCC2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 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, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 5, 9, 15, 15, 15, 15, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 5, 5, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 62 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 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: 102 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312549 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC(=O)N2CCCCC2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 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, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 12, 5, 5, 5, 5, 17, 26, 39, 39, 39, 39, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 12, 12, 17, 17, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 62 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 227 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312549 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC(=O)N2CCCCC2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 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, 7, 7, 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, 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: [23, 23, 19, 12, 12, 7, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 23, 23, 23, 19, 19, 7, 7, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 25 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 113 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312549 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312549/1 /scratch/stefan/7770667/working/building/REAL300020312549 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/42 `/scratch/stefan/7770667/working/3D/42' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC(=O)N2CCCCC2C1) `REAL300020312549.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312549/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312549 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC(=O)N2CCCCC2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 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, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 5, 9, 15, 15, 15, 15, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 5, 5, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 62 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 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: 102 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312549 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC(=O)N2CCCCC2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 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, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 12, 5, 5, 5, 5, 17, 26, 39, 39, 39, 39, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 12, 12, 17, 17, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 62 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 227 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312549 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC(=O)N2CCCCC2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 7, 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, 7, 7, 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, 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: [23, 23, 19, 12, 12, 7, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 23, 23, 23, 19, 19, 7, 7, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 25 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 113 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312549 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312549 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312549/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312549/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312549 Building REAL300020312550 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312550' /scratch/stefan/7770667/working/building/REAL300020312550 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312550 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312550/0 /scratch/stefan/7770667/working/building/REAL300020312550 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/43 `/scratch/stefan/7770667/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC(=O)N2CCCCC2C1) `REAL300020312550.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312550 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC(=O)N2CCCCC2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 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, 7, 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, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 37 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312550 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC(=O)N2CCCCC2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 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, 7, 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, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 12, 5, 5, 5, 5, 13, 19, 19, 19, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 12, 12, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 37 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 123 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312550 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC(=O)N2CCCCC2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 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, 7, 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, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 22, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 33, 33, 33, 22, 22, 3, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 37 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 156 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312550 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312550/1 /scratch/stefan/7770667/working/building/REAL300020312550 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/44 `/scratch/stefan/7770667/working/3D/44' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC(=O)N2CCCCC2C1) `REAL300020312550.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312550 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC(=O)N2CCCCC2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 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, 7, 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, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 37 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312550 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC(=O)N2CCCCC2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 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, 7, 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, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 12, 5, 5, 5, 5, 13, 19, 19, 19, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 12, 12, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 37 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 123 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312550 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC(=O)N2CCCCC2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 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, 7, 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, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 22, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 33, 33, 33, 22, 22, 3, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 37 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 156 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312550 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312550 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312550/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312550/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312550 Building REAL300020312551 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312551' /scratch/stefan/7770667/working/building/REAL300020312551 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312551 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312551/0 /scratch/stefan/7770667/working/building/REAL300020312551 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/45 `/scratch/stefan/7770667/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(C=CCO2)CC1) `REAL300020312551.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312551 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(C=CCO2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 1, 5, 12, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 6, 1, 1, 1, 1, 5, 9, 15, 15, 15, 15, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 6, 6, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 61 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 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: 105 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312551 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(C=CCO2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 1, 5, 12, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 13, 5, 5, 5, 5, 18, 26, 33, 33, 33, 33, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 13, 13, 18, 18, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 61 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 218 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312551 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(C=CCO2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 1, 5, 12, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 17, 11, 11, 7, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 18, 18, 18, 18, 18, 18, 18, 18, 18, 20, 20, 20, 17, 17, 7, 7, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 21 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 100 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312551 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312551/1 /scratch/stefan/7770667/working/building/REAL300020312551 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/46 `/scratch/stefan/7770667/working/3D/46' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(C=CCO2)CC1) `REAL300020312551.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312551/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312551 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(C=CCO2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 1, 5, 12, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 6, 1, 1, 1, 1, 5, 9, 15, 15, 15, 15, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 6, 6, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 61 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 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: 105 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312551 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(C=CCO2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 1, 5, 12, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 13, 5, 5, 5, 5, 18, 26, 33, 33, 33, 33, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 13, 13, 18, 18, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 61 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 218 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312551 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(C=CCO2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 1, 5, 12, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 18, 12, 12, 7, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 21, 21, 21, 18, 18, 7, 7, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 22 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 102 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312551 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312551 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312551/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312551/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312551 Building REAL300020312552 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312552' /scratch/stefan/7770667/working/building/REAL300020312552 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312552 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312552/0 /scratch/stefan/7770667/working/building/REAL300020312552 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/47 `/scratch/stefan/7770667/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(C=CCO2)CC1) `REAL300020312552.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312552 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(C=CCO2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.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', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 1, 5, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 6, 1, 1, 1, 1, 7, 9, 9, 9, 9, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 6, 6, 7, 7, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 36 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 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: 79 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312552 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(C=CCO2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.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', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 1, 5, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 13, 5, 5, 5, 5, 15, 20, 20, 20, 20, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 13, 13, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 36 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 121 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312552 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(C=CCO2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.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', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 1, 5, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 22, 9, 9, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 31, 31, 31, 22, 22, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 36 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 142 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312552 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312552/1 /scratch/stefan/7770667/working/building/REAL300020312552 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/48 `/scratch/stefan/7770667/working/3D/48' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(C=CCO2)CC1) `REAL300020312552.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312552/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312552 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(C=CCO2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.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', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 1, 5, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 6, 1, 1, 1, 1, 7, 9, 9, 9, 9, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 6, 6, 7, 7, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 36 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 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: 79 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312552 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(C=CCO2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.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', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 1, 5, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 13, 5, 5, 5, 5, 15, 20, 20, 20, 20, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 13, 13, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 36 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 121 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312552 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(C=CCO2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.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', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 1, 5, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 22, 9, 9, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 31, 31, 31, 22, 22, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 36 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 142 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312552 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312552 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312552/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312552/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312552 Building REAL300020312553 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312553' /scratch/stefan/7770667/working/building/REAL300020312553 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312553 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312553/0 /scratch/stefan/7770667/working/building/REAL300020312553 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/49 `/scratch/stefan/7770667/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N(CC)CC1CCOCC1) `REAL300020312553.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312553 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N(CC)CC1CCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 9, 5, 1, 1, 1, 1, 5, 8, 13, 13, 13, 13, 1, 1, 1, 1, 5, 14, 5, 15, 38, 38, 38, 38, 37, 9, 9, 9, 5, 5, 5, 5, 8, 8, 14, 14, 14, 14, 14, 15, 15, 38, 38, 38, 38, 38, 38, 38, 38, 38] 201 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 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: 243 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312553 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N(CC)CC1CCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [80, 80, 65, 38, 38, 38, 38, 113, 131, 156, 156, 156, 156, 38, 38, 19, 9, 19, 46, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 65, 65, 113, 113, 131, 131, 46, 46, 46, 46, 46, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 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]) total number of confs: 908 number of broken/clashed sets: 27 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312553 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N(CC)CC1CCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 29, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 42, 98, 42, 109, 148, 148, 148, 148, 146, 30, 30, 30, 29, 29, 6, 6, 4, 4, 98, 98, 98, 98, 98, 109, 109, 148, 148, 148, 148, 148, 148, 148, 148, 148] 186 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 895 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312553 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312553/1 /scratch/stefan/7770667/working/building/REAL300020312553 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/50 `/scratch/stefan/7770667/working/3D/50' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N(CC)CC1CCOCC1) `REAL300020312553.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312553 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N(CC)CC1CCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 9, 5, 1, 1, 1, 1, 5, 8, 13, 13, 13, 13, 1, 1, 1, 1, 5, 14, 5, 15, 38, 38, 38, 38, 37, 9, 9, 9, 5, 5, 5, 5, 8, 8, 14, 14, 14, 14, 14, 15, 15, 38, 38, 38, 38, 38, 38, 38, 38, 38] 201 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 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: 243 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312553 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N(CC)CC1CCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [81, 81, 65, 38, 38, 38, 38, 112, 130, 157, 157, 157, 157, 38, 38, 19, 9, 19, 46, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 65, 65, 112, 112, 130, 130, 46, 46, 46, 46, 46, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 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]) total number of confs: 915 number of broken/clashed sets: 27 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312553 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N(CC)CC1CCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 28, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 41, 97, 41, 110, 149, 149, 149, 149, 147, 29, 29, 29, 28, 28, 6, 6, 4, 4, 97, 97, 97, 97, 97, 110, 110, 149, 149, 149, 149, 149, 149, 149, 149, 149] 187 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 900 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312553 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312553 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312553/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312553/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312553 Building REAL300020312554 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312554' /scratch/stefan/7770667/working/building/REAL300020312554 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312554 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312554/0 /scratch/stefan/7770667/working/building/REAL300020312554 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/51 `/scratch/stefan/7770667/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(CC)CC1CCOCC1) `REAL300020312554.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312554 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(CC)CC1CCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 5, 1, 1, 1, 1, 5, 8, 8, 8, 8, 1, 1, 1, 1, 4, 11, 4, 11, 22, 22, 22, 22, 21, 9, 9, 9, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22] 80 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 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: 167 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312554 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(CC)CC1CCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 37, 22, 22, 22, 22, 42, 54, 54, 54, 54, 22, 22, 13, 7, 13, 19, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 37, 37, 42, 42, 19, 19, 19, 19, 19, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1] 80 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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]) total number of confs: 369 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312554 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(CC)CC1CCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 16, 8, 8, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 16, 31, 16, 34, 54, 54, 54, 54, 53, 22, 22, 22, 16, 16, 3, 3, 31, 31, 31, 31, 31, 34, 34, 54, 54, 54, 54, 54, 54, 54, 54, 54] 80 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 328 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312554 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312554/1 /scratch/stefan/7770667/working/building/REAL300020312554 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/52 `/scratch/stefan/7770667/working/3D/52' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(CC)CC1CCOCC1) `REAL300020312554.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312554 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(CC)CC1CCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 5, 1, 1, 1, 1, 5, 8, 8, 8, 8, 1, 1, 1, 1, 4, 11, 4, 11, 22, 22, 22, 22, 21, 9, 9, 9, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22] 80 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 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: 167 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312554 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(CC)CC1CCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 37, 22, 22, 22, 22, 42, 54, 54, 54, 54, 22, 22, 13, 7, 13, 19, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 37, 37, 42, 42, 19, 19, 19, 19, 19, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1] 80 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 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]) total number of confs: 369 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312554 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(CC)CC1CCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 16, 8, 8, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 16, 31, 16, 34, 54, 54, 54, 54, 53, 22, 22, 22, 16, 16, 3, 3, 31, 31, 31, 31, 31, 34, 34, 54, 54, 54, 54, 54, 54, 54, 54, 54] 80 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 328 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312554 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312554 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312554/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312554/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312554 Building REAL300020312555 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312555' /scratch/stefan/7770667/working/building/REAL300020312555 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312555 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312555/0 /scratch/stefan/7770667/working/building/REAL300020312555 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/53 `/scratch/stefan/7770667/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(CC1)OC(=O)NC2(C)C) `REAL300020312555.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312555 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(CC1)OC(=O)NC2(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 5, 5, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 64 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 104 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312555 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(CC1)OC(=O)NC2(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 12, 5, 5, 5, 5, 18, 29, 36, 36, 36, 36, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 12, 12, 18, 18, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 64 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 239 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312555 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(CC1)OC(=O)NC2(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 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] dock color type numbers: [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, 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, 20, 13, 13, 8, 4, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 23, 23, 23, 20, 20, 8, 8, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 24 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 108 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312555 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312555/1 /scratch/stefan/7770667/working/building/REAL300020312555 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/54 `/scratch/stefan/7770667/working/3D/54' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(CC1)OC(=O)NC2(C)C) `REAL300020312555.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312555 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(CC1)OC(=O)NC2(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 5, 5, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 64 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 104 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312555 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(CC1)OC(=O)NC2(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 12, 5, 5, 5, 5, 18, 29, 36, 36, 36, 36, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 12, 12, 18, 18, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 64 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 239 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312555 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(CC1)OC(=O)NC2(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 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] dock color type numbers: [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, 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, 20, 14, 14, 8, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 23, 23, 23, 20, 20, 8, 8, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 24 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 102 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312555 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312555 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312555/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312555/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312555 Building REAL300020312556 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312556' /scratch/stefan/7770667/working/building/REAL300020312556 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312556 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312556/0 /scratch/stefan/7770667/working/building/REAL300020312556 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/55 `/scratch/stefan/7770667/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(CC1)OC(=O)NC2(C)C) `REAL300020312556.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312556 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(CC1)OC(=O)NC2(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [11, 11, 5, 1, 1, 1, 1, 7, 10, 10, 10, 10, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 5, 5, 7, 7, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 42 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 78 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312556 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(CC1)OC(=O)NC2(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [20, 20, 12, 5, 5, 5, 5, 17, 24, 24, 24, 24, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 12, 12, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 42 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 152 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312556 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(CC1)OC(=O)NC2(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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, 24, 10, 10, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 37, 37, 37, 24, 24, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 42 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 176 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312556 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312556/1 /scratch/stefan/7770667/working/building/REAL300020312556 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/56 `/scratch/stefan/7770667/working/3D/56' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(CC1)OC(=O)NC2(C)C) `REAL300020312556.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312556 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(CC1)OC(=O)NC2(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [11, 11, 5, 1, 1, 1, 1, 7, 10, 10, 10, 10, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 5, 5, 7, 7, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 42 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 78 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312556 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(CC1)OC(=O)NC2(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [20, 20, 12, 5, 5, 5, 5, 17, 24, 24, 24, 24, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 12, 12, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 42 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 152 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312556 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(CC1)OC(=O)NC2(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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, 24, 10, 10, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 37, 37, 37, 24, 24, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24] 42 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 176 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312556 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312556 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312556/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312556/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312556 Building REAL300020312557 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312557' /scratch/stefan/7770667/working/building/REAL300020312557 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312557 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312557/0 /scratch/stefan/7770667/working/building/REAL300020312557 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/57 `/scratch/stefan/7770667/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N(C)CCC1=NC(C)=CS1) `REAL300020312557.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312557 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N(C)CCC1=NC(C)=CS1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 8, 1, 5, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 1, 1, 1, 1, 4, 4, 11, 18, 76, 76, 76, 76, 76, 7, 7, 7, 5, 5, 5, 5, 5, 5, 4, 4, 4, 11, 11, 18, 18, 76, 76, 76, 76] 201 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 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: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312557 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N(C)CCC1=NC(C)=CS1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 8, 1, 5, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 110, 76, 76, 76, 76, 176, 176, 184, 184, 184, 184, 76, 76, 42, 15, 42, 8, 1, 1, 1, 1, 1, 1, 1, 113, 113, 113, 110, 110, 176, 176, 176, 176, 42, 42, 42, 15, 15, 8, 8, 2, 2, 2, 1] 201 rigid atoms, others: [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, 41, 42, 43, 44]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312557 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N(C)CCC1=NC(C)=CS1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 8, 1, 5, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 11, 11, 4, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 28, 28, 71, 86, 185, 185, 185, 185, 185, 24, 24, 24, 23, 23, 4, 4, 4, 4, 28, 28, 28, 71, 71, 86, 86, 185, 185, 185, 185] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 569 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312557 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312557/1 /scratch/stefan/7770667/working/building/REAL300020312557 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/58 `/scratch/stefan/7770667/working/3D/58' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N(C)CCC1=NC(C)=CS1) `REAL300020312557.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312557 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N(C)CCC1=NC(C)=CS1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 8, 1, 5, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 1, 1, 1, 1, 4, 4, 11, 18, 76, 76, 76, 76, 76, 7, 7, 7, 5, 5, 5, 5, 5, 5, 4, 4, 4, 11, 11, 18, 18, 76, 76, 76, 76] 201 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 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: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312557 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N(C)CCC1=NC(C)=CS1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 8, 1, 5, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 109, 76, 76, 76, 76, 177, 177, 185, 185, 185, 185, 76, 76, 42, 15, 42, 8, 1, 1, 1, 1, 1, 1, 1, 112, 112, 112, 109, 109, 177, 177, 177, 177, 42, 42, 42, 15, 15, 8, 8, 2, 2, 2, 1] 201 rigid atoms, others: [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, 41, 42, 43, 44]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312557 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N(C)CCC1=NC(C)=CS1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 8, 1, 5, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 11, 11, 4, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 28, 28, 72, 88, 185, 185, 185, 185, 185, 24, 24, 24, 23, 23, 4, 4, 4, 4, 28, 28, 28, 72, 72, 88, 88, 185, 185, 185, 185] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 575 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312557 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312557 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312557/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312557/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312557 Building REAL300020312558 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312558' /scratch/stefan/7770667/working/building/REAL300020312558 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312558 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312558/0 /scratch/stefan/7770667/working/building/REAL300020312558 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/59 `/scratch/stefan/7770667/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(C)CCC1=NC(C)=CS1) `REAL300020312558.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312558 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(C)CCC1=NC(C)=CS1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 8, 1, 5, 1, 14, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 3, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 13, 20, 76, 76, 76, 76, 76, 10, 10, 10, 5, 5, 3, 3, 4, 4, 4, 13, 13, 20, 20, 76, 76, 76, 76] 201 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 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: 215 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312558 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(C)CCC1=NC(C)=CS1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 8, 1, 5, 1, 14, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 125, 76, 76, 76, 76, 119, 146, 146, 146, 146, 76, 76, 40, 17, 40, 8, 1, 1, 1, 1, 1, 1, 1, 142, 142, 142, 125, 125, 119, 119, 40, 40, 40, 17, 18, 8, 8, 2, 2, 2, 1] 201 rigid atoms, others: [42, 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]) total number of confs: 853 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312558 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(C)CCC1=NC(C)=CS1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 8, 1, 5, 1, 14, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 6, 5, 3, 1, 1, 1, 1, 1, 1, 5, 6, 6, 6, 14, 14, 37, 50, 146, 146, 146, 146, 146, 20, 20, 20, 14, 14, 3, 3, 14, 14, 14, 37, 37, 50, 50, 146, 146, 146, 146] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 419 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312558 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312558/1 /scratch/stefan/7770667/working/building/REAL300020312558 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/60 `/scratch/stefan/7770667/working/3D/60' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(C)CCC1=NC(C)=CS1) `REAL300020312558.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312558 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(C)CCC1=NC(C)=CS1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 8, 1, 5, 1, 14, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 3, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 13, 20, 75, 75, 75, 75, 75, 10, 10, 10, 5, 5, 3, 3, 4, 4, 4, 13, 13, 20, 20, 75, 75, 75, 75] 201 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 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: 214 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312558 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(C)CCC1=NC(C)=CS1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 8, 1, 5, 1, 14, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 125, 75, 75, 75, 75, 120, 147, 147, 147, 147, 75, 75, 40, 17, 40, 8, 1, 1, 1, 1, 1, 1, 1, 141, 141, 141, 125, 125, 120, 120, 40, 40, 40, 17, 17, 8, 8, 2, 2, 2, 1] 201 rigid atoms, others: [42, 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]) total number of confs: 862 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312558 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(C)CCC1=NC(C)=CS1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 8, 1, 5, 1, 14, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 6, 6, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 14, 14, 37, 50, 147, 147, 147, 147, 147, 20, 20, 20, 14, 14, 3, 3, 14, 14, 14, 37, 37, 50, 50, 147, 147, 147, 147] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 416 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312558 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312558 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312558/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312558/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312558 Building REAL300020312559 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312559' /scratch/stefan/7770667/working/building/REAL300020312559 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312559 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312559/0 /scratch/stefan/7770667/working/building/REAL300020312559 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/61 `/scratch/stefan/7770667/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCCCNS(=O)(=O)CC1) `REAL300020312559.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312559 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCCCNS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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] 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: [5, 5, 3, 1, 1, 1, 1, 5, 9, 12, 12, 12, 12, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 3, 3, 5, 5, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 28 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 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: 71 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312559 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCCCNS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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] 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: [10, 10, 6, 4, 4, 4, 4, 11, 16, 19, 19, 19, 19, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 6, 6, 11, 11, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 28 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 107 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312559 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCCCNS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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] 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, 15, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 15, 15, 5, 5, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 17 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 78 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312559 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312559/1 /scratch/stefan/7770667/working/building/REAL300020312559 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/62 `/scratch/stefan/7770667/working/3D/62' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCCCNS(=O)(=O)CC1) `REAL300020312559.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312559 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCCCNS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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] 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: [5, 5, 3, 1, 1, 1, 1, 5, 9, 12, 12, 12, 12, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 3, 3, 5, 5, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 28 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 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: 71 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312559 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCCCNS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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] 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: [10, 10, 6, 4, 4, 4, 4, 11, 16, 19, 19, 19, 19, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 6, 6, 11, 11, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 28 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 107 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312559 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCCCNS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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] 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, 15, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 17, 17, 17, 15, 15, 5, 5, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 17 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 78 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312559 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312559 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312559/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312559/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312559 Building REAL300020312560 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312560' /scratch/stefan/7770667/working/building/REAL300020312560 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312560 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312560/0 /scratch/stefan/7770667/working/building/REAL300020312560 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/63 `/scratch/stefan/7770667/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCCCNS(=O)(=O)CC1) `REAL300020312560.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312560 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCCCNS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 5, 5, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 33 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 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: 70 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312560 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCCCNS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 11, 5, 5, 5, 5, 13, 19, 19, 19, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 11, 11, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 33 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 114 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312560 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCCCNS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 21, 8, 8, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 30, 30, 30, 21, 21, 3, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 33 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 137 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312560 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312560/1 /scratch/stefan/7770667/working/building/REAL300020312560 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/64 `/scratch/stefan/7770667/working/3D/64' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCCCNS(=O)(=O)CC1) `REAL300020312560.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312560 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCCCNS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 5, 5, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 33 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 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: 70 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312560 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCCCNS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 11, 5, 5, 5, 5, 13, 19, 19, 19, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 11, 11, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 33 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 114 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312560 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCCCNS(=O)(=O)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 14, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 21, 8, 8, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 30, 30, 30, 21, 21, 3, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 33 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 137 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312560 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312560 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312560/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312560/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312560 Building REAL300020312561 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312561' /scratch/stefan/7770667/working/building/REAL300020312561 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312561 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312561/0 /scratch/stefan/7770667/working/building/REAL300020312561 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/65 `/scratch/stefan/7770667/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1C[C@@H]2C[C@H](C(=O)OC)C[C@@H]2C1) `REAL300020312561.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312561 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1C[C@@H]2C[C@H](C(=O)OC)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 1, 11, 12, 5, 5, 5, 7, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 4, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 6, 6, 6, 6, 10, 10, 10, 4, 4, 5, 5, 9, 9, 6, 6, 6, 6, 16, 16, 16, 6, 6, 6, 6] 120 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 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: 118 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312561 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1C[C@@H]2C[C@H](C(=O)OC)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 1, 11, 12, 5, 5, 5, 7, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 14, 6, 6, 6, 6, 18, 30, 30, 30, 30, 30, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 20, 20, 20, 14, 14, 18, 18, 30, 30, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1] 120 rigid atoms, others: [48, 49, 40, 41, 42, 43, 50, 47, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46]) total number of confs: 201 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312561 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1C[C@@H]2C[C@H](C(=O)OC)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 1, 11, 12, 5, 5, 5, 7, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 17, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 28, 28, 28, 28, 28, 28, 28, 69, 69, 69, 28, 28, 28, 28, 20, 20, 20, 17, 17, 6, 6, 4, 4, 28, 28, 28, 28, 69, 69, 69, 28, 28, 28, 28] 88 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 232 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312561 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312561/1 /scratch/stefan/7770667/working/building/REAL300020312561 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/66 `/scratch/stefan/7770667/working/3D/66' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1C[C@@H]2C[C@H](C(=O)OC)C[C@@H]2C1) `REAL300020312561.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312561 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1C[C@@H]2C[C@H](C(=O)OC)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 1, 11, 12, 5, 5, 5, 7, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 4, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 6, 6, 6, 6, 10, 10, 10, 4, 4, 5, 5, 9, 9, 6, 6, 6, 6, 16, 16, 16, 6, 6, 6, 6] 119 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 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: 118 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312561 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1C[C@@H]2C[C@H](C(=O)OC)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 1, 11, 12, 5, 5, 5, 7, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 14, 6, 6, 6, 6, 18, 30, 30, 30, 30, 30, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 20, 20, 20, 14, 14, 18, 18, 30, 30, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1] 119 rigid atoms, others: [48, 49, 40, 41, 42, 43, 50, 47, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46]) total number of confs: 201 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312561 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1C[C@@H]2C[C@H](C(=O)OC)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 1, 11, 12, 5, 5, 5, 7, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 88 conformations in input total number of sets (complete confs): 88 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 18, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 29, 29, 29, 29, 29, 29, 29, 69, 69, 69, 29, 29, 29, 29, 21, 21, 21, 18, 18, 6, 6, 4, 4, 29, 29, 29, 29, 69, 69, 69, 29, 29, 29, 29] 88 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 236 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312561 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312561 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312561/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312561/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312561 Building REAL300020312562 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312562' /scratch/stefan/7770667/working/building/REAL300020312562 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312562 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312562/0 /scratch/stefan/7770667/working/building/REAL300020312562 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/67 `/scratch/stefan/7770667/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1C[C@@H]2C[C@H](C(=O)OC)C[C@@H]2C1) `REAL300020312562.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312562 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1C[C@@H]2C[C@H](C(=O)OC)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 1, 11, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 6, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 6, 6, 6, 6, 12, 12, 12, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 6, 6, 6, 6] 172 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 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: 107 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312562 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1C[C@@H]2C[C@H](C(=O)OC)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 1, 11, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 18, 6, 6, 6, 6, 19, 28, 28, 28, 28, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 33, 33, 33, 18, 18, 19, 19, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1] 172 rigid atoms, others: [37, 38, 39, 40, 47, 46, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43]) total number of confs: 219 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312562 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1C[C@@H]2C[C@H](C(=O)OC)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 1, 11, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 21, 6, 6, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 60, 60, 60, 22, 22, 22, 22, 27, 27, 27, 21, 21, 3, 3, 22, 22, 22, 22, 60, 60, 60, 22, 22, 22, 22] 142 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 245 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312562 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312562/1 /scratch/stefan/7770667/working/building/REAL300020312562 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/68 `/scratch/stefan/7770667/working/3D/68' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1C[C@@H]2C[C@H](C(=O)OC)C[C@@H]2C1) `REAL300020312562.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312562 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1C[C@@H]2C[C@H](C(=O)OC)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 1, 11, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 6, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 6, 6, 6, 6, 12, 12, 12, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 6, 6, 6, 6] 173 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 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: 107 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312562 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1C[C@@H]2C[C@H](C(=O)OC)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 1, 11, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 18, 6, 6, 6, 6, 19, 28, 28, 28, 28, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 33, 33, 33, 18, 18, 19, 19, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1] 173 rigid atoms, others: [37, 38, 39, 40, 47, 46, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43]) total number of confs: 219 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312562 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1C[C@@H]2C[C@H](C(=O)OC)C[C@@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 1, 11, 12, 5, 5, 5, 7, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 21, 6, 6, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 22, 22, 22, 22, 22, 22, 22, 61, 61, 61, 22, 22, 22, 22, 27, 27, 27, 21, 21, 3, 3, 22, 22, 22, 22, 61, 61, 61, 22, 22, 22, 22] 142 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 249 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312562 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312562 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312562/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312562/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312562 Building REAL300020312563 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312563' /scratch/stefan/7770667/working/building/REAL300020312563 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312563 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312563/0 /scratch/stefan/7770667/working/building/REAL300020312563 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/69 `/scratch/stefan/7770667/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(C(=O)OC)(C2CCC2)C1) `REAL300020312563.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312563 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(C(=O)OC)(C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 7] 0 hydrogens 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, 42, 18, 18, 18, 18, 54, 68, 88, 88, 88, 88, 18, 18, 5, 5, 5, 5, 1, 5, 12, 12, 12, 1, 1, 1, 1, 5, 63, 63, 63, 42, 42, 54, 54, 68, 68, 5, 5, 5, 5, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 5, 5] 201 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 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, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 52, 53]) total number of confs: 544 number of broken/clashed sets: 12 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312563 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(C(=O)OC)(C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 5, 7, 11, 11, 11, 11, 1, 1, 1, 1, 6, 6, 6, 6, 24, 24, 24, 6, 18, 18, 18, 6, 10, 10, 10, 4, 4, 5, 5, 7, 7, 6, 6, 6, 6, 24, 24, 24, 18, 18, 18, 18, 18, 18, 18, 6, 6] 201 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 164 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312563 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(C(=O)OC)(C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 7] 0 hydrogens 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, 14, 6, 6, 6, 6, 20, 26, 35, 35, 35, 35, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 1, 5, 5, 5, 1, 23, 23, 23, 14, 14, 20, 20, 26, 26, 1, 1, 1, 1, 7, 7, 7, 5, 5, 5, 5, 5, 5, 5, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 53, 24, 52, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 226 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312563 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(C(=O)OC)(C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 7] 0 hydrogens 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, 39, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 46, 46, 46, 46, 131, 131, 131, 46, 86, 86, 86, 46, 52, 52, 52, 39, 39, 6, 6, 4, 4, 46, 46, 46, 46, 131, 131, 131, 86, 86, 86, 86, 86, 86, 86, 46, 46] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 622 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312563 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312563/1 /scratch/stefan/7770667/working/building/REAL300020312563 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/70 `/scratch/stefan/7770667/working/3D/70' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(C(=O)OC)(C2CCC2)C1) `REAL300020312563.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312563/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312563 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(C(=O)OC)(C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 7] 0 hydrogens 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, 42, 18, 18, 18, 18, 54, 68, 88, 88, 88, 88, 18, 18, 5, 5, 5, 5, 1, 5, 12, 12, 12, 1, 1, 1, 1, 5, 63, 63, 63, 42, 42, 54, 54, 68, 68, 5, 5, 5, 5, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 5, 5] 201 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 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, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 52, 53]) total number of confs: 544 number of broken/clashed sets: 12 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312563 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(C(=O)OC)(C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 7] 0 hydrogens 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, 4, 1, 1, 1, 1, 5, 7, 11, 11, 11, 11, 1, 1, 1, 1, 6, 6, 6, 6, 24, 24, 24, 6, 18, 18, 18, 6, 10, 10, 10, 4, 4, 5, 5, 7, 7, 6, 6, 6, 6, 24, 24, 24, 18, 18, 18, 18, 18, 18, 18, 6, 6] 201 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 164 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312563 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(C(=O)OC)(C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 7] 0 hydrogens 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, 14, 6, 6, 6, 6, 20, 26, 35, 35, 35, 35, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 1, 5, 5, 5, 1, 23, 23, 23, 14, 14, 20, 20, 26, 26, 1, 1, 1, 1, 7, 7, 7, 5, 5, 5, 5, 5, 5, 5, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 53, 24, 52, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 226 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312563 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(C(=O)OC)(C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 7] 0 hydrogens 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, 39, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 46, 46, 46, 46, 131, 131, 131, 46, 86, 86, 86, 46, 52, 52, 52, 39, 39, 6, 6, 4, 4, 46, 46, 46, 46, 131, 131, 131, 86, 86, 86, 86, 86, 86, 86, 46, 46] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 621 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312563 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312563 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312563/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312563/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312563 Building REAL300020312564 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312564' /scratch/stefan/7770667/working/building/REAL300020312564 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312564 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312564/0 /scratch/stefan/7770667/working/building/REAL300020312564 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/71 `/scratch/stefan/7770667/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(C(=O)OC)(C2CCC2)C1) `REAL300020312564.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312564 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(C(=O)OC)(C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 38, 18, 18, 18, 18, 27, 41, 41, 41, 41, 18, 18, 5, 5, 5, 5, 1, 5, 12, 12, 12, 1, 1, 1, 1, 5, 47, 47, 47, 38, 38, 27, 27, 5, 5, 5, 5, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 5, 5] 104 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 18, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 49, 50]) total number of confs: 271 number of broken/clashed sets: 9 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312564 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(C(=O)OC)(C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 5, 1, 1, 1, 1, 3, 5, 5, 5, 5, 1, 1, 1, 1, 6, 6, 6, 6, 24, 24, 24, 6, 18, 18, 18, 6, 9, 9, 9, 5, 5, 3, 3, 6, 6, 6, 6, 24, 24, 24, 18, 18, 18, 18, 18, 18, 18, 6, 6] 104 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 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: 139 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312564 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(C(=O)OC)(C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 13, 6, 6, 6, 6, 9, 15, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 1, 5, 5, 5, 1, 20, 20, 20, 13, 13, 9, 9, 1, 1, 1, 1, 7, 7, 7, 5, 5, 5, 5, 5, 5, 5, 1, 1] 104 rigid atoms, others: [35, 36, 37, 38, 49, 50, 14, 15, 16, 17, 18, 19, 23, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 133 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312564 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(C(=O)OC)(C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 16, 5, 5, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 15, 15, 15, 15, 57, 57, 57, 15, 41, 41, 41, 15, 20, 20, 20, 16, 16, 3, 3, 15, 15, 15, 15, 57, 57, 57, 41, 41, 41, 41, 41, 41, 41, 15, 15] 104 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 282 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312564 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312564/1 /scratch/stefan/7770667/working/building/REAL300020312564 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/72 `/scratch/stefan/7770667/working/3D/72' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(C(=O)OC)(C2CCC2)C1) `REAL300020312564.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312564/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312564 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(C(=O)OC)(C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 38, 18, 18, 18, 18, 27, 41, 41, 41, 41, 18, 18, 5, 5, 5, 5, 1, 5, 12, 12, 12, 1, 1, 1, 1, 5, 47, 47, 47, 38, 38, 27, 27, 5, 5, 5, 5, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 5, 5] 103 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 18, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 49, 50]) total number of confs: 271 number of broken/clashed sets: 9 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312564 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(C(=O)OC)(C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 5, 1, 1, 1, 1, 3, 5, 5, 5, 5, 1, 1, 1, 1, 6, 6, 6, 6, 24, 24, 24, 6, 18, 18, 18, 6, 9, 9, 9, 5, 5, 3, 3, 6, 6, 6, 6, 24, 24, 24, 18, 18, 18, 18, 18, 18, 18, 6, 6] 103 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 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: 139 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312564 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(C(=O)OC)(C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 13, 6, 6, 6, 6, 9, 15, 15, 15, 15, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 1, 5, 5, 5, 1, 20, 20, 20, 13, 13, 9, 9, 1, 1, 1, 1, 7, 7, 7, 5, 5, 5, 5, 5, 5, 5, 1, 1] 103 rigid atoms, others: [35, 36, 37, 38, 49, 50, 14, 15, 16, 17, 18, 19, 23, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 133 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312564 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(C(=O)OC)(C2CCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 11, 12, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 16, 5, 5, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 15, 15, 15, 15, 56, 56, 56, 15, 41, 41, 41, 15, 20, 20, 20, 16, 16, 3, 3, 15, 15, 15, 15, 56, 56, 56, 41, 41, 41, 41, 41, 41, 41, 15, 15] 103 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 280 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312564 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312564 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312564/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312564/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312564 Building REAL300020312565 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312565' /scratch/stefan/7770667/working/building/REAL300020312565 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312565 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312565/0 /scratch/stefan/7770667/working/building/REAL300020312565 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/73 `/scratch/stefan/7770667/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(C1)CCCCO2) `REAL300020312565.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312565 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(C1)CCCCO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 12, 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, 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 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 4, 1, 1, 1, 1, 6, 10, 16, 16, 16, 16, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 4, 4, 6, 6, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 81 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 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: 103 number of broken/clashed sets: 81 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312565 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(C1)CCCCO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 12, 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, 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 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 17, 6, 6, 6, 6, 24, 34, 51, 51, 51, 51, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 17, 17, 24, 24, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 81 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 305 number of broken/clashed sets: 81 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312565 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(C1)CCCCO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 12, 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, 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 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 11, 11, 7, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 17, 17, 17, 17, 17, 7, 7, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 23 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 79 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312565 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312565/1 /scratch/stefan/7770667/working/building/REAL300020312565 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/74 `/scratch/stefan/7770667/working/3D/74' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(C1)CCCCO2) `REAL300020312565.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312565/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312565 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(C1)CCCCO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 12, 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, 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 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 6, 10, 16, 16, 16, 16, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 5, 5, 6, 6, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 82 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 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: 106 number of broken/clashed sets: 82 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312565 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(C1)CCCCO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 12, 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, 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 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 18, 6, 6, 6, 6, 24, 34, 51, 51, 51, 51, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 18, 18, 24, 24, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 82 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 308 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312565 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(C1)CCCCO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 12, 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, 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 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 11, 11, 7, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 17, 17, 17, 17, 17, 7, 7, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 23 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 79 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312565 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312565 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312565/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312565/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312565 Building REAL300020312566 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312566' /scratch/stefan/7770667/working/building/REAL300020312566 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312566 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312566/0 /scratch/stefan/7770667/working/building/REAL300020312566 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/75 `/scratch/stefan/7770667/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(C1)CCCCO2) `REAL300020312566.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312566 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(C1)CCCCO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 12, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 7, 9, 9, 9, 9, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 5, 5, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 53 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 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: 77 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312566 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(C1)CCCCO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 12, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 18, 6, 6, 6, 6, 18, 27, 27, 27, 27, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 53 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 187 number of broken/clashed sets: 53 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312566 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(C1)CCCCO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 12, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 24, 9, 9, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 37, 37, 37, 24, 24, 3, 3, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 53 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 176 number of broken/clashed sets: 53 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312566 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312566/1 /scratch/stefan/7770667/working/building/REAL300020312566 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/76 `/scratch/stefan/7770667/working/3D/76' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(C1)CCCCO2) `REAL300020312566.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312566/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312566 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(C1)CCCCO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 12, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 7, 9, 9, 9, 9, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 5, 5, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 53 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 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: 77 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312566 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(C1)CCCCO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 12, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 18, 6, 6, 6, 6, 18, 27, 27, 27, 27, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 53 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 187 number of broken/clashed sets: 53 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312566 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(C1)CCCCO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 12, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 24, 9, 9, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 37, 37, 37, 24, 24, 3, 3, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 53 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 176 number of broken/clashed sets: 53 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312566 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312566 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312566/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312566/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312566 Building REAL300020312567 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312567' /scratch/stefan/7770667/working/building/REAL300020312567 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312567 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312567/0 /scratch/stefan/7770667/working/building/REAL300020312567 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/77 `/scratch/stefan/7770667/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(F)(C(F)(F)F)C1) `REAL300020312567.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312567 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(F)(C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'F', 'F', 'F', 'C.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 15, 5, 15, 15, 15, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 11, 5, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 5, 5, 5, 5, 9, 9, 6, 6, 6, 6, 6, 6] 78 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 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: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312567 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(F)(C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'F', 'F', 'F', 'C.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 15, 5, 15, 15, 15, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 30, 15, 6, 6, 6, 6, 24, 36, 49, 49, 49, 49, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 30, 30, 30, 15, 15, 24, 24, 36, 36, 1, 1, 1, 1, 1, 1] 78 rigid atoms, others: [35, 36, 37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312567 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(F)(C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'F', 'F', 'F', 'C.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 15, 5, 15, 15, 15, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 26, 24, 13, 13, 8, 4, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 24, 24, 24, 24, 24, 24, 24, 24, 24, 26, 26, 26, 24, 24, 8, 8, 4, 4, 24, 24, 24, 24, 24, 24] 34 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312567 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312567/1 /scratch/stefan/7770667/working/building/REAL300020312567 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/78 `/scratch/stefan/7770667/working/3D/78' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(F)(C(F)(F)F)C1) `REAL300020312567.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312567/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312567 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(F)(C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'F', 'F', 'F', 'C.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 15, 5, 15, 15, 15, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 11, 5, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 5, 5, 5, 5, 9, 9, 6, 6, 6, 6, 6, 6] 78 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 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: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312567 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(F)(C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'F', 'F', 'F', 'C.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 15, 5, 15, 15, 15, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [30, 30, 15, 6, 6, 6, 6, 24, 36, 49, 49, 49, 49, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 30, 30, 30, 15, 15, 24, 24, 36, 36, 1, 1, 1, 1, 1, 1] 78 rigid atoms, others: [35, 36, 37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312567 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(F)(C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'F', 'F', 'F', 'C.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 15, 5, 15, 15, 15, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 26, 24, 13, 13, 8, 4, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 24, 24, 24, 24, 24, 24, 24, 24, 24, 26, 26, 26, 24, 24, 8, 8, 4, 4, 24, 24, 24, 24, 24, 24] 34 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312567 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312567 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312567/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312567/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312567 Building REAL300020312568 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312568' /scratch/stefan/7770667/working/building/REAL300020312568 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312568 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312568/0 /scratch/stefan/7770667/working/building/REAL300020312568 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/79 `/scratch/stefan/7770667/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(F)(C(F)(F)F)C1) `REAL300020312568.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312568 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(F)(C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 15, 5, 15, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 10, 4, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6] 48 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 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: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312568 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(F)(C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 15, 5, 15, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 28, 16, 6, 6, 6, 6, 15, 24, 24, 24, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 28, 28, 28, 16, 16, 15, 15, 1, 1, 1, 1, 1, 1] 48 rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312568 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(F)(C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 15, 5, 15, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 34, 22, 8, 8, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 34, 34, 34, 22, 22, 3, 3, 24, 24, 24, 24, 24, 24] 48 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312568 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312568/1 /scratch/stefan/7770667/working/building/REAL300020312568 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/80 `/scratch/stefan/7770667/working/3D/80' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(F)(C(F)(F)F)C1) `REAL300020312568.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312568 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(F)(C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 15, 5, 15, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 10, 4, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6] 48 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 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: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312568 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(F)(C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 15, 5, 15, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [28, 28, 16, 6, 6, 6, 6, 15, 24, 24, 24, 24, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 28, 28, 28, 16, 16, 15, 15, 1, 1, 1, 1, 1, 1] 48 rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 20, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312568 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(F)(C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 15, 5, 15, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 34, 22, 8, 8, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 34, 34, 34, 22, 22, 3, 3, 24, 24, 24, 24, 24, 24] 48 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 163 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312568 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312568 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312568/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312568/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312568 Building REAL300020312569 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312569' /scratch/stefan/7770667/working/building/REAL300020312569 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312569 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312569/0 /scratch/stefan/7770667/working/building/REAL300020312569 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/81 `/scratch/stefan/7770667/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1C[C@H]2OC[C@@H](C(=O)OC)[C@H]2C1) `REAL300020312569.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312569 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1C[C@H]2OC[C@@H](C(=O)OC)[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 7, 1, 11, 12, 5, 5, 7, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 5, 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 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 5, 1, 1, 1, 1, 6, 10, 11, 11, 11, 11, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 6, 6, 6, 6, 6, 6, 5, 5, 6, 6, 10, 10, 6, 6, 6, 6, 8, 8, 8, 6, 6] 34 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312569 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1C[C@H]2OC[C@@H](C(=O)OC)[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 7, 1, 11, 12, 5, 5, 7, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 5, 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 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 6, 6, 6, 6, 14, 22, 23, 23, 23, 23, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 13, 13, 13, 13, 13, 14, 14, 22, 22, 1, 1, 1, 1, 3, 3, 3, 1, 1] 34 rigid atoms, others: [48, 40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312569 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1C[C@H]2OC[C@@H](C(=O)OC)[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 7, 1, 11, 12, 5, 5, 7, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 5, 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 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 19, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 33, 33, 33, 28, 28, 28, 22, 22, 22, 19, 19, 6, 6, 4, 4, 28, 28, 28, 28, 33, 33, 33, 28, 28] 47 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 135 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312569 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312569/1 /scratch/stefan/7770667/working/building/REAL300020312569 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/82 `/scratch/stefan/7770667/working/3D/82' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1C[C@H]2OC[C@@H](C(=O)OC)[C@H]2C1) `REAL300020312569.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312569/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312569 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1C[C@H]2OC[C@@H](C(=O)OC)[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 7, 1, 11, 12, 5, 5, 7, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 5, 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 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 5, 1, 1, 1, 1, 6, 10, 11, 11, 11, 11, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 6, 6, 6, 6, 6, 6, 5, 5, 6, 6, 10, 10, 6, 6, 6, 6, 8, 8, 8, 6, 6] 32 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312569 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1C[C@H]2OC[C@@H](C(=O)OC)[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 7, 1, 11, 12, 5, 5, 7, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 5, 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 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 6, 6, 6, 6, 14, 21, 22, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 13, 13, 13, 13, 13, 14, 14, 21, 21, 1, 1, 1, 1, 3, 3, 3, 1, 1] 32 rigid atoms, others: [48, 40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 47, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312569 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1C[C@H]2OC[C@@H](C(=O)OC)[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 7, 1, 11, 12, 5, 5, 7, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 5, 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 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 19, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 33, 33, 33, 28, 28, 28, 22, 22, 22, 19, 19, 6, 6, 4, 4, 28, 28, 28, 28, 33, 33, 33, 28, 28] 47 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 135 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312569 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312569 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312569/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312569/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312569 Building REAL300020312570 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312570' /scratch/stefan/7770667/working/building/REAL300020312570 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312570 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312570/0 /scratch/stefan/7770667/working/building/REAL300020312570 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/83 `/scratch/stefan/7770667/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1C[C@H]2OC[C@@H](C(=O)OC)[C@H]2C1) `REAL300020312570.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312570 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1C[C@H]2OC[C@@H](C(=O)OC)[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 7, 1, 11, 12, 5, 5, 7, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 5, 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 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 5, 5, 5, 11, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 5, 5] 69 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312570 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1C[C@H]2OC[C@@H](C(=O)OC)[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 7, 1, 11, 12, 5, 5, 7, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 5, 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 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 15, 5, 5, 5, 5, 16, 24, 24, 24, 24, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 31, 30, 30, 15, 15, 16, 16, 1, 1, 1, 1, 3, 3, 3, 1, 1] 69 rigid atoms, others: [37, 38, 39, 40, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312570 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1C[C@H]2OC[C@@H](C(=O)OC)[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 7, 1, 11, 12, 5, 5, 7, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 5, 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 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 15, 6, 6, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 26, 26, 26, 17, 17, 17, 20, 20, 20, 15, 15, 3, 3, 17, 17, 17, 17, 26, 26, 26, 17, 17] 47 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312570 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312570/1 /scratch/stefan/7770667/working/building/REAL300020312570 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/84 `/scratch/stefan/7770667/working/3D/84' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1C[C@H]2OC[C@@H](C(=O)OC)[C@H]2C1) `REAL300020312570.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312570/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312570 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1C[C@H]2OC[C@@H](C(=O)OC)[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 7, 1, 11, 12, 5, 5, 7, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 5, 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 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 5, 5, 5, 11, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 5, 5] 69 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312570 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1C[C@H]2OC[C@@H](C(=O)OC)[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 7, 1, 11, 12, 5, 5, 7, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 5, 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 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 15, 5, 5, 5, 5, 16, 24, 24, 24, 24, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 31, 30, 30, 15, 15, 16, 16, 1, 1, 1, 1, 3, 3, 3, 1, 1] 69 rigid atoms, others: [37, 38, 39, 40, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312570 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1C[C@H]2OC[C@@H](C(=O)OC)[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 7, 1, 11, 12, 5, 5, 7, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 5, 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 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 15, 6, 6, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 26, 26, 26, 17, 17, 17, 20, 20, 20, 15, 15, 3, 3, 17, 17, 17, 17, 26, 26, 26, 17, 17] 47 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312570 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312570 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312570/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312570/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312570 Building REAL300020312571 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312571' /scratch/stefan/7770667/working/building/REAL300020312571 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312571 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312571/0 /scratch/stefan/7770667/working/building/REAL300020312571 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/85 `/scratch/stefan/7770667/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(C1)OC(=O)NC2(C)C) `REAL300020312571.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312571 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(C1)OC(=O)NC2(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 4, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 4, 4, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6] 83 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 113 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312571 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(C1)OC(=O)NC2(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 13, 5, 5, 5, 5, 22, 36, 48, 48, 48, 48, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 13, 13, 22, 22, 36, 36, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 83 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48, 49]) total number of confs: 309 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312571 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(C1)OC(=O)NC2(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [29, 29, 26, 14, 14, 8, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 29, 29, 29, 26, 26, 8, 8, 4, 4, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 39 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 146 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312571 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312571/1 /scratch/stefan/7770667/working/building/REAL300020312571 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/86 `/scratch/stefan/7770667/working/3D/86' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(C1)OC(=O)NC2(C)C) `REAL300020312571.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312571 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(C1)OC(=O)NC2(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [10, 10, 4, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 4, 4, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6] 84 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 113 number of broken/clashed sets: 84 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312571 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(C1)OC(=O)NC2(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [28, 28, 13, 5, 5, 5, 5, 22, 36, 48, 48, 48, 48, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 13, 13, 22, 22, 36, 36, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 84 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46, 47, 48, 49]) total number of confs: 309 number of broken/clashed sets: 84 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312571 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(C1)OC(=O)NC2(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [29, 29, 26, 14, 14, 8, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 29, 29, 29, 26, 26, 8, 8, 4, 4, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 39 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 146 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312571 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312571 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312571/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312571/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312571 Building REAL300020312572 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312572' /scratch/stefan/7770667/working/building/REAL300020312572 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312572 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312572/0 /scratch/stefan/7770667/working/building/REAL300020312572 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/87 `/scratch/stefan/7770667/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(C1)OC(=O)NC2(C)C) `REAL300020312572.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312572 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(C1)OC(=O)NC2(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [11, 11, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 46 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 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: 74 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312572 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(C1)OC(=O)NC2(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [28, 28, 16, 6, 6, 6, 6, 14, 22, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 16, 16, 14, 14, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 46 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46]) total number of confs: 182 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312572 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(C1)OC(=O)NC2(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 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: [34, 34, 22, 8, 8, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 34, 34, 34, 22, 22, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 46 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 161 number of broken/clashed sets: 46 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312572 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312572/1 /scratch/stefan/7770667/working/building/REAL300020312572 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/88 `/scratch/stefan/7770667/working/3D/88' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(C1)OC(=O)NC2(C)C) `REAL300020312572.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312572/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312572 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(C1)OC(=O)NC2(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 47 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 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: 74 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312572 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(C1)OC(=O)NC2(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 16, 6, 6, 6, 6, 14, 22, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 16, 16, 14, 14, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2] 47 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 44, 45, 46]) total number of confs: 188 number of broken/clashed sets: 47 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312572 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(C1)OC(=O)NC2(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 22, 8, 8, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 34, 34, 34, 22, 22, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 47 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 161 number of broken/clashed sets: 47 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312572 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312572 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312572/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312572/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312572 Building REAL300020312573 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312573' /scratch/stefan/7770667/working/building/REAL300020312573 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312573 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312573/0 /scratch/stefan/7770667/working/building/REAL300020312573 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/89 `/scratch/stefan/7770667/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC=CCC2(CCOCC2)C1) `REAL300020312573.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312573 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC=CCC2(CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 12, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 5, 1, 1, 1, 1, 5, 9, 15, 15, 15, 15, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 5, 5, 5, 5, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 60 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 95 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312573 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC=CCC2(CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 12, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 11, 4, 4, 4, 4, 16, 25, 35, 35, 35, 35, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 11, 11, 16, 16, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 60 rigid atoms, others: [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, 49, 50, 51, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 214 number of broken/clashed sets: 60 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312573 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC=CCC2(CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 12, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 18, 11, 11, 7, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 20, 20, 20, 18, 18, 7, 7, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 24 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 99 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312573 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312573/1 /scratch/stefan/7770667/working/building/REAL300020312573 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/90 `/scratch/stefan/7770667/working/3D/90' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC=CCC2(CCOCC2)C1) `REAL300020312573.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312573 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC=CCC2(CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 12, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 5, 1, 1, 1, 1, 5, 9, 15, 15, 15, 15, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 5, 5, 5, 5, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 60 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 95 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312573 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC=CCC2(CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 12, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 11, 4, 4, 4, 4, 16, 25, 35, 35, 35, 35, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 11, 11, 16, 16, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 60 rigid atoms, others: [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, 49, 50, 51, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 214 number of broken/clashed sets: 60 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312573 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC=CCC2(CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 12, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 18, 11, 11, 7, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 20, 20, 20, 18, 18, 7, 7, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 24 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 99 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312573 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312573 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312573/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312573/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312573 Building REAL300020312574 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312574' /scratch/stefan/7770667/working/building/REAL300020312574 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312574 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312574/0 /scratch/stefan/7770667/working/building/REAL300020312574 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/91 `/scratch/stefan/7770667/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC=CCC2(CCOCC2)C1) `REAL300020312574.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312574 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC=CCC2(CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 5, 1, 1, 1, 1, 4, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 28 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 60 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312574 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC=CCC2(CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 10, 4, 4, 4, 4, 11, 17, 17, 17, 17, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 10, 10, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 28 rigid atoms, others: [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] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 33, 27, 28, 29, 30, 31]) total number of confs: 104 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312574 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC=CCC2(CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 19, 6, 6, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 24, 24, 24, 19, 19, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 29 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 118 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312574 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312574/1 /scratch/stefan/7770667/working/building/REAL300020312574 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/92 `/scratch/stefan/7770667/working/3D/92' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC=CCC2(CCOCC2)C1) `REAL300020312574.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312574 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC=CCC2(CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 5, 1, 1, 1, 1, 4, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 28 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 60 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312574 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC=CCC2(CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 10, 4, 4, 4, 4, 11, 17, 17, 17, 17, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 10, 10, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 28 rigid atoms, others: [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] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 33, 27, 28, 29, 30, 31]) total number of confs: 104 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312574 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC=CCC2(CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 20, 6, 6, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 25, 25, 25, 20, 20, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 30 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 121 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312574 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312574 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312574/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312574/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312574 Building REAL300020312575 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312575' /scratch/stefan/7770667/working/building/REAL300020312575 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312575 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312575/0 /scratch/stefan/7770667/working/building/REAL300020312575 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/93 `/scratch/stefan/7770667/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(C)[C@H]1CC[C@H](C2=CC=CC=C2)CC1) `REAL300020312575.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312575 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(C)[C@H]1CC[C@H](C2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [39, 39, 31, 16, 16, 16, 16, 34, 45, 45, 45, 45, 16, 16, 10, 3, 10, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 39, 39, 39, 31, 31, 34, 34, 10, 10, 10, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3] 68 rigid atoms, others: [45, 46, 47, 48, 49, 21, 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, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 50, 51, 52, 53]) total number of confs: 270 number of broken/clashed sets: 33 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312575 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(C)[C@H]1CC[C@H](C2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 9, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 10, 16, 16, 16, 16, 16, 10, 10, 9, 9, 9, 5, 5, 6, 6, 4, 4, 4, 10, 10, 10, 10, 16, 16, 16, 16, 16, 10, 10, 10, 10] 68 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 100 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312575 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(C)[C@H]1CC[C@H](C2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 29, 21, 10, 10, 10, 10, 23, 34, 34, 34, 34, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 1, 1, 29, 29, 29, 21, 21, 23, 23, 7, 7, 7, 1, 1, 1, 1, 3, 3, 2, 3, 3, 1, 1, 1, 1] 68 rigid atoms, others: [51, 41, 42, 43, 44, 50, 15, 17, 18, 19, 20, 21, 22, 23, 52, 29, 30, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 215 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312575 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(C)[C@H]1CC[C@H](C2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 26, 18, 8, 8, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 18, 18, 34, 34, 34, 34, 34, 34, 45, 45, 45, 45, 45, 34, 34, 26, 26, 26, 18, 18, 3, 3, 18, 18, 18, 34, 34, 34, 34, 45, 45, 45, 45, 45, 34, 34, 34, 34] 68 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 218 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312575 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312575/1 /scratch/stefan/7770667/working/building/REAL300020312575 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/94 `/scratch/stefan/7770667/working/3D/94' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(C)[C@H]1CC[C@H](C2=CC=CC=C2)CC1) `REAL300020312575.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312575/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312575 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(C)[C@H]1CC[C@H](C2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [39, 39, 31, 16, 16, 16, 16, 34, 46, 46, 46, 46, 16, 16, 10, 3, 10, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 39, 39, 39, 31, 31, 34, 34, 10, 10, 10, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3] 68 rigid atoms, others: [45, 46, 47, 48, 49, 21, 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, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 50, 51, 52, 53]) total number of confs: 272 number of broken/clashed sets: 31 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312575 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(C)[C@H]1CC[C@H](C2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 9, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 4, 4, 10, 10, 10, 10, 10, 10, 16, 16, 16, 16, 16, 10, 10, 9, 9, 9, 5, 5, 6, 6, 4, 4, 4, 10, 10, 10, 10, 16, 16, 16, 16, 16, 10, 10, 10, 10] 68 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 100 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312575 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(C)[C@H]1CC[C@H](C2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 29, 21, 10, 10, 10, 10, 23, 34, 34, 34, 34, 10, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 1, 1, 29, 29, 29, 21, 21, 23, 23, 7, 7, 7, 1, 1, 1, 1, 3, 3, 2, 3, 3, 1, 1, 1, 1] 68 rigid atoms, others: [51, 41, 42, 43, 44, 50, 15, 17, 18, 19, 20, 21, 22, 23, 52, 29, 30, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49]) total number of confs: 215 number of broken/clashed sets: 31 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312575 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(C)[C@H]1CC[C@H](C2=CC=CC=C2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 26, 18, 8, 8, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 18, 18, 34, 34, 34, 34, 34, 34, 46, 46, 46, 46, 46, 34, 34, 26, 26, 26, 18, 18, 3, 3, 18, 18, 18, 34, 34, 34, 34, 46, 46, 46, 46, 46, 34, 34, 34, 34] 68 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 220 number of broken/clashed sets: 31 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312575 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312575 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312575/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312575/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312575 Building REAL300020312576 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312576' /scratch/stefan/7770667/working/building/REAL300020312576 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312576 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312576/0 /scratch/stefan/7770667/working/building/REAL300020312576 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/95 `/scratch/stefan/7770667/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2=C(C1)C(C(=O)OCC)=NO2) `REAL300020312576.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312576 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2=C(C1)C(C(=O)OCC)=NO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 1, 5, 1, 1, 11, 12, 5, 5, 8, 12, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 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 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 4, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 13, 13, 16, 25, 3, 3, 7, 7, 7, 4, 4, 5, 5, 3, 3, 3, 3, 3, 3, 25, 25, 25, 25, 25] 78 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 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: 131 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312576 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2=C(C1)C(C(=O)OCC)=NO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 1, 5, 1, 1, 11, 12, 5, 5, 8, 12, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 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 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 6, 3, 3, 3, 3, 8, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 16, 1, 1, 9, 9, 9, 6, 6, 8, 8, 1, 1, 1, 1, 1, 1, 16, 16, 17, 17, 17] 78 rigid atoms, others: [36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46]) total number of confs: 126 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312576 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2=C(C1)C(C(=O)OCC)=NO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 1, 5, 1, 1, 11, 12, 5, 5, 8, 12, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 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 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 15, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 12, 38, 38, 45, 57, 12, 12, 21, 21, 21, 15, 15, 3, 3, 12, 12, 12, 12, 12, 12, 57, 57, 57, 57, 57] 79 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 242 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312576 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312576/1 /scratch/stefan/7770667/working/building/REAL300020312576 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/96 `/scratch/stefan/7770667/working/3D/96' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2=C(C1)C(C(=O)OCC)=NO2) `REAL300020312576.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312576 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2=C(C1)C(C(=O)OCC)=NO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 1, 5, 1, 1, 11, 12, 5, 5, 8, 12, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 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 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 4, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 13, 13, 17, 26, 3, 3, 7, 7, 7, 4, 4, 5, 5, 3, 3, 3, 3, 3, 3, 26, 26, 26, 26, 26] 79 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 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: 133 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312576 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2=C(C1)C(C(=O)OCC)=NO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 1, 5, 1, 1, 11, 12, 5, 5, 8, 12, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 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 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 6, 3, 3, 3, 3, 8, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 17, 1, 1, 9, 9, 9, 6, 6, 8, 8, 1, 1, 1, 1, 1, 1, 17, 17, 18, 18, 18] 79 rigid atoms, others: [36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 42, 43, 44, 45, 46]) total number of confs: 128 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312576 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2=C(C1)C(C(=O)OCC)=NO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 1, 5, 1, 1, 11, 12, 5, 5, 8, 12, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 3, 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 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 15, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 12, 38, 38, 45, 57, 12, 12, 21, 21, 21, 15, 15, 3, 3, 12, 12, 12, 12, 12, 12, 57, 57, 57, 57, 57] 79 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 242 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312576 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312576 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312576/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312576/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312576 Building REAL300020312577 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312577' /scratch/stefan/7770667/working/building/REAL300020312577 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312577 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312577/0 /scratch/stefan/7770667/working/building/REAL300020312577 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/97 `/scratch/stefan/7770667/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC[C@@]2(CO)CCCC[C@H]12) `REAL300020312577.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312577 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC[C@@]2(CO)CCCC[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 5, 1, 1, 1, 1, 6, 10, 11, 11, 11, 11, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 5, 5, 6, 6, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 9, 3, 3, 3, 3, 3, 3, 3, 3] 99 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 96 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312577 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC[C@@]2(CO)CCCC[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 7, 3, 3, 3, 3, 11, 18, 20, 20, 20, 20, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 7, 7, 11, 11, 18, 18, 1, 1, 1, 1, 1, 1, 2, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1] 99 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 47, 48, 49, 50, 51, 52, 53, 54] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 134 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312577 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC[C@@]2(CO)CCCC[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 28, 11, 11, 5, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 29, 29, 29, 28, 28, 5, 5, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 60, 20, 20, 20, 20, 20, 20, 20, 20] 96 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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, 54]) total number of confs: 193 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312577 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312577/1 /scratch/stefan/7770667/working/building/REAL300020312577 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/98 `/scratch/stefan/7770667/working/3D/98' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC[C@@]2(CO)CCCC[C@H]12) `REAL300020312577.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312577 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC[C@@]2(CO)CCCC[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 5, 1, 1, 1, 1, 6, 10, 11, 11, 11, 11, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 5, 5, 6, 6, 10, 10, 3, 3, 3, 3, 3, 3, 3, 3, 9, 3, 3, 3, 3, 3, 3, 3, 3] 102 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 96 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312577 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC[C@@]2(CO)CCCC[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 102 conformations in input total number of sets (complete confs): 102 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 7, 3, 3, 3, 3, 11, 19, 21, 21, 21, 21, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 7, 7, 11, 11, 19, 19, 1, 1, 1, 1, 1, 1, 2, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1] 102 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 47, 48, 49, 50, 51, 52, 53, 54] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46]) total number of confs: 140 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312577 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC[C@@]2(CO)CCCC[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 5, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 28, 11, 11, 5, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 29, 29, 29, 28, 28, 5, 5, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 63, 21, 21, 21, 21, 21, 21, 21, 21] 99 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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, 54]) total number of confs: 198 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312577 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312577 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312577/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312577/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312577 Building REAL300020312578 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312578' /scratch/stefan/7770667/working/building/REAL300020312578 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312578 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312578/0 /scratch/stefan/7770667/working/building/REAL300020312578 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/99 `/scratch/stefan/7770667/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC[C@@]2(CO)CCCC[C@H]12) `REAL300020312578.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312578 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC[C@@]2(CO)CCCC[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 1 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: [9, 9, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 9, 3, 3, 3, 3, 3, 3, 3, 3] 72 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: 71 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312578 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC[C@@]2(CO)CCCC[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 1 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: [11, 11, 7, 3, 3, 3, 3, 10, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 11, 11, 11, 7, 7, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1] 72 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43]) total number of confs: 93 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312578 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC[C@@]2(CO)CCCC[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 1 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: [23, 23, 19, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 23, 23, 23, 19, 19, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 42, 14, 14, 14, 14, 14, 14, 14, 14] 75 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 148 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312578 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312578/1 /scratch/stefan/7770667/working/building/REAL300020312578 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/100 `/scratch/stefan/7770667/working/3D/100' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC[C@@]2(CO)CCCC[C@H]12) `REAL300020312578.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312578 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC[C@@]2(CO)CCCC[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 1 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: [9, 9, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 9, 3, 3, 3, 3, 3, 3, 3, 3] 75 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: 71 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312578 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC[C@@]2(CO)CCCC[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 1 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: [12, 12, 8, 3, 3, 3, 3, 10, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 12, 12, 12, 8, 8, 10, 10, 1, 1, 1, 1, 1, 1, 2, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1] 75 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43]) total number of confs: 96 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312578 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC[C@@]2(CO)CCCC[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 1 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: [23, 23, 19, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 23, 23, 23, 19, 19, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 42, 14, 14, 14, 14, 14, 14, 14, 14] 75 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 148 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312578 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312578 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312578/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312578/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312578 Building REAL300020312579 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312579' /scratch/stefan/7770667/working/building/REAL300020312579 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312579 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312579/0 /scratch/stefan/7770667/working/building/REAL300020312579 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/101 `/scratch/stefan/7770667/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC[C@@]2(CO)CCC[C@@H]12) `REAL300020312579.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312579 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC[C@@]2(CO)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 5, 1, 1, 1, 1, 5, 9, 14, 14, 14, 14, 1, 1, 1, 1, 3, 3, 3, 3, 3, 8, 3, 3, 3, 3, 3, 9, 9, 9, 5, 5, 5, 5, 9, 9, 3, 3, 3, 3, 3, 3, 8, 8, 24, 3, 3, 3, 3, 3, 3] 159 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: 137 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312579 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC[C@@]2(CO)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 7, 3, 3, 3, 3, 11, 17, 26, 26, 26, 26, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 11, 11, 11, 7, 7, 11, 11, 17, 17, 1, 1, 1, 1, 1, 1, 5, 5, 15, 1, 1, 1, 1, 1, 1] 159 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 46, 47, 48, 49, 50, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 160 number of broken/clashed sets: 74 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312579 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC[C@@]2(CO)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 1 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: [47, 47, 37, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 26, 26, 26, 26, 26, 40, 26, 26, 26, 26, 26, 47, 47, 47, 37, 37, 6, 6, 4, 4, 26, 26, 26, 26, 26, 26, 40, 40, 120, 26, 26, 26, 26, 26, 26] 156 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 420 number of broken/clashed sets: 73 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312579 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312579/1 /scratch/stefan/7770667/working/building/REAL300020312579 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/102 `/scratch/stefan/7770667/working/3D/102' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC[C@@]2(CO)CCC[C@@H]12) `REAL300020312579.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312579/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312579 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC[C@@]2(CO)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 5, 1, 1, 1, 1, 5, 9, 14, 14, 14, 14, 1, 1, 1, 1, 3, 3, 3, 3, 3, 8, 3, 3, 3, 3, 3, 9, 9, 9, 5, 5, 5, 5, 9, 9, 3, 3, 3, 3, 3, 3, 8, 8, 24, 3, 3, 3, 3, 3, 3] 159 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: 137 number of broken/clashed sets: 74 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312579 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC[C@@]2(CO)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 7, 3, 3, 3, 3, 11, 17, 26, 26, 26, 26, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 1, 1, 11, 11, 11, 7, 7, 11, 11, 17, 17, 1, 1, 1, 1, 1, 1, 5, 5, 15, 1, 1, 1, 1, 1, 1] 159 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 46, 47, 48, 49, 50, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45]) total number of confs: 160 number of broken/clashed sets: 74 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312579 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC[C@@]2(CO)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 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] dock color type numbers: [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, 7, 7, 7, 7, 7, 7] 1 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: [47, 47, 37, 16, 16, 6, 4, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 26, 26, 26, 26, 26, 40, 26, 26, 26, 26, 26, 47, 47, 47, 37, 37, 6, 6, 4, 4, 26, 26, 26, 26, 26, 26, 40, 40, 120, 26, 26, 26, 26, 26, 26] 156 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 420 number of broken/clashed sets: 73 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312579 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312579 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312579/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312579/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312579 Building REAL300020312580 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312580' /scratch/stefan/7770667/working/building/REAL300020312580 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312580 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312580/0 /scratch/stefan/7770667/working/building/REAL300020312580 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/103 `/scratch/stefan/7770667/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC[C@@]2(CO)CCC[C@@H]12) `REAL300020312580.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312580 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC[C@@]2(CO)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 1 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: [9, 9, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 3, 3, 6, 3, 3, 3, 3, 3, 9, 9, 9, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 18, 3, 3, 3, 3, 3, 3] 84 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 95 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312580 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC[C@@]2(CO)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 1 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: [10, 10, 6, 3, 3, 3, 3, 9, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 1, 1, 1, 1, 1, 10, 10, 10, 6, 6, 9, 9, 1, 1, 1, 1, 1, 1, 4, 4, 12, 1, 1, 1, 1, 1, 1] 84 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42]) total number of confs: 99 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312580 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC[C@@]2(CO)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 1 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: [27, 27, 21, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 13, 13, 21, 13, 13, 13, 13, 13, 27, 27, 27, 21, 21, 3, 3, 13, 13, 13, 13, 13, 13, 21, 21, 63, 13, 13, 13, 13, 13, 13] 84 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 234 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312580 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312580/1 /scratch/stefan/7770667/working/building/REAL300020312580 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/104 `/scratch/stefan/7770667/working/3D/104' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC[C@@]2(CO)CCC[C@@H]12) `REAL300020312580.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312580/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312580 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC[C@@]2(CO)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 1 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: [9, 9, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 3, 3, 6, 3, 3, 3, 3, 3, 9, 9, 9, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 6, 6, 18, 3, 3, 3, 3, 3, 3] 84 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 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: 95 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312580 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC[C@@]2(CO)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 1 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: [10, 10, 6, 3, 3, 3, 3, 9, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 1, 1, 1, 1, 1, 10, 10, 10, 6, 6, 9, 9, 1, 1, 1, 1, 1, 1, 4, 4, 12, 1, 1, 1, 1, 1, 1] 84 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42]) total number of confs: 99 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312580 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC[C@@]2(CO)CCC[C@@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 1 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: [27, 27, 21, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 13, 13, 21, 13, 13, 13, 13, 13, 27, 27, 27, 21, 21, 3, 3, 13, 13, 13, 13, 13, 13, 21, 21, 63, 13, 13, 13, 13, 13, 13] 84 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 234 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312580 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312580 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312580/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312580/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312580 Building REAL300020312581 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312581' /scratch/stefan/7770667/working/building/REAL300020312581 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312581 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312581/0 /scratch/stefan/7770667/working/building/REAL300020312581 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/105 `/scratch/stefan/7770667/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1NC1=NN(CCC)C=C1) `REAL300020312581.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312581 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1NC1=NN(CCC)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 8, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 5, 7, 12, 12, 12, 12, 1, 1, 1, 1, 6, 13, 13, 13, 49, 68, 13, 13, 5, 5, 5, 3, 3, 5, 5, 7, 7, 6, 49, 49, 68, 68, 68, 68, 68, 13, 13] 201 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312581 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1NC1=NN(CCC)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 8, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 13, 13, 13, 13, 47, 51, 74, 74, 74, 74, 13, 13, 4, 1, 1, 1, 1, 1, 8, 14, 1, 1, 32, 32, 32, 22, 22, 47, 47, 51, 51, 4, 8, 8, 14, 14, 14, 14, 14, 1, 1] 201 rigid atoms, others: [42, 43, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312581 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1NC1=NN(CCC)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 8, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 42, 75, 75, 75, 160, 177, 75, 75, 32, 32, 32, 21, 21, 6, 6, 4, 4, 42, 160, 160, 177, 177, 177, 177, 177, 75, 75] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 752 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312581 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312581/1 /scratch/stefan/7770667/working/building/REAL300020312581 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/106 `/scratch/stefan/7770667/working/3D/106' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1NC1=NN(CCC)C=C1) `REAL300020312581.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312581/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312581 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1NC1=NN(CCC)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 8, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 5, 7, 12, 12, 12, 12, 1, 1, 1, 1, 6, 13, 13, 13, 49, 68, 13, 13, 5, 5, 5, 3, 3, 5, 5, 7, 7, 6, 49, 49, 68, 68, 68, 68, 68, 13, 13] 201 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312581 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1NC1=NN(CCC)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 8, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 13, 13, 13, 13, 47, 51, 74, 74, 74, 74, 13, 13, 4, 1, 1, 1, 1, 1, 8, 14, 1, 1, 32, 32, 32, 22, 22, 47, 47, 51, 51, 4, 8, 8, 14, 14, 14, 14, 14, 1, 1] 201 rigid atoms, others: [42, 43, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312581 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1NC1=NN(CCC)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 8, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 41, 75, 75, 75, 160, 177, 75, 75, 32, 32, 32, 21, 21, 6, 6, 4, 4, 41, 160, 160, 177, 177, 177, 177, 177, 75, 75] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 759 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312581 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312581 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312581/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312581/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312581 Building REAL300020312582 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312582' /scratch/stefan/7770667/working/building/REAL300020312582 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312582 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312582/0 /scratch/stefan/7770667/working/building/REAL300020312582 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/107 `/scratch/stefan/7770667/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1NC1=NN(CCC)C=C1) `REAL300020312582.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312582 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1NC1=NN(CCC)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 8, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 1, 1, 1, 1, 2, 4, 4, 4, 4, 1, 1, 1, 1, 9, 20, 20, 20, 53, 59, 20, 20, 4, 5, 5, 2, 2, 2, 2, 9, 53, 53, 59, 59, 59, 59, 59, 20, 20] 201 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312582 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1NC1=NN(CCC)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 8, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 20, 20, 20, 20, 34, 49, 49, 49, 49, 20, 20, 4, 1, 1, 1, 1, 1, 8, 14, 1, 1, 45, 45, 45, 34, 34, 34, 34, 4, 8, 8, 14, 14, 14, 14, 14, 1, 1] 201 rigid atoms, others: [39, 40, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 346 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312582 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1NC1=NN(CCC)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 8, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 4, 4, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 22, 41, 41, 41, 106, 109, 41, 41, 15, 15, 15, 8, 8, 3, 3, 22, 106, 106, 109, 109, 109, 109, 109, 41, 41] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 443 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312582 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312582/1 /scratch/stefan/7770667/working/building/REAL300020312582 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/108 `/scratch/stefan/7770667/working/3D/108' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1NC1=NN(CCC)C=C1) `REAL300020312582.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312582/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312582 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1NC1=NN(CCC)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 8, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 1, 1, 1, 1, 9, 20, 20, 20, 53, 59, 20, 20, 5, 5, 5, 2, 2, 2, 2, 9, 53, 53, 59, 59, 59, 59, 59, 20, 20] 201 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312582 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1NC1=NN(CCC)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 8, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 20, 20, 20, 20, 34, 49, 49, 49, 49, 20, 20, 4, 1, 1, 1, 1, 1, 8, 14, 1, 1, 45, 45, 45, 34, 34, 34, 34, 4, 8, 8, 14, 14, 14, 14, 14, 1, 1] 201 rigid atoms, others: [39, 40, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 346 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312582 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1NC1=NN(CCC)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 8, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 5, 5, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 23, 42, 42, 42, 107, 110, 42, 42, 15, 15, 15, 9, 9, 4, 4, 23, 107, 107, 110, 110, 110, 110, 110, 42, 42] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 443 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312582 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312582 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312582/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312582/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312582 Building REAL300020312583 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312583' /scratch/stefan/7770667/working/building/REAL300020312583 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312583 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312583/0 /scratch/stefan/7770667/working/building/REAL300020312583 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/109 `/scratch/stefan/7770667/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(NC2=NN(CCC)C=C2)=NN=C1C1=CC=C(C2=NN=N[N-]2)C=C1) `REAL300020312583.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312583 none C#CCCN1C(NC2=NN(CCC)C=C2)=NN=C1C1=CC=C(C2=NN=N[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.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: [1, 1, 5, 5, 8, 1, 8, 1, 8, 8, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 10, 10, 10, 10, 35, 85, 85, 85, 151, 158, 85, 85, 10, 10, 1, 1, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 31, 31, 31, 19, 19, 35, 151, 151, 158, 158, 158, 158, 158, 85, 85, 4, 4, 4, 4] 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]) total number of confs: 660 number of broken/clashed sets: 25 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312583 none C#CCCN1C(NC2=NN(CCC)C=C2)=NN=C1C1=CC=C(C2=NN=N[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.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: [1, 1, 5, 5, 8, 1, 8, 1, 8, 8, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 1, 1, 1, 7, 21, 21, 21, 78, 106, 21, 21, 1, 1, 1, 1, 4, 4, 1, 1, 10, 10, 10, 10, 4, 4, 10, 10, 10, 6, 6, 7, 78, 78, 106, 106, 106, 106, 106, 21, 21, 4, 4, 4, 4] 201 rigid atoms, others: [3, 4, 5, 6, 15, 16, 17, 18] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 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: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312583 none C#CCCN1C(NC2=NN(CCC)C=C2)=NN=C1C1=CC=C(C2=NN=N[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.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: [1, 1, 5, 5, 8, 1, 8, 1, 8, 8, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 4, 4, 4, 4, 18, 52, 52, 52, 122, 135, 52, 52, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 20, 20, 20, 12, 12, 18, 122, 122, 135, 135, 135, 135, 135, 52, 52, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 17, 18, 19, 20, 21, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 565 number of broken/clashed sets: 25 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312583 none C#CCCN1C(NC2=NN(CCC)C=C2)=NN=C1C1=CC=C(C2=NN=N[N-]2)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.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: [1, 1, 5, 5, 8, 1, 8, 1, 8, 8, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 21, 21, 7, 1, 1, 1, 1, 1, 9, 17, 1, 1, 21, 21, 21, 21, 52, 52, 21, 21, 83, 83, 83, 83, 52, 52, 63, 63, 63, 40, 40, 7, 9, 9, 17, 17, 17, 17, 17, 1, 1, 52, 52, 52, 52] 201 rigid atoms, others: [6, 7, 8, 9, 10, 43, 13, 14, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 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, 44, 45, 46, 47]) total number of confs: 533 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312583 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312583/1 /scratch/stefan/7770667/working/building/REAL300020312583 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/110 `/scratch/stefan/7770667/working/3D/110' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(NC2=NN(CCC)C=C2)=NN=C1C1=CC=C(C2=N[N-]N=N2)C=C1) `REAL300020312583.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312583 none C#CCCN1C(NC2=NN(CCC)C=C2)=NN=C1C1=CC=C(C2=N[N-]N=N2)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.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: [1, 1, 5, 5, 8, 1, 8, 1, 8, 8, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 10, 10, 10, 10, 35, 85, 85, 85, 150, 158, 85, 85, 10, 10, 2, 2, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 31, 31, 31, 19, 19, 35, 150, 150, 158, 158, 158, 158, 158, 85, 85, 4, 4, 4, 4] 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]) total number of confs: 664 number of broken/clashed sets: 24 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312583 none C#CCCN1C(NC2=NN(CCC)C=C2)=NN=C1C1=CC=C(C2=N[N-]N=N2)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.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: [1, 1, 5, 5, 8, 1, 8, 1, 8, 8, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 1, 1, 1, 7, 21, 21, 21, 76, 104, 21, 21, 1, 1, 1, 1, 4, 4, 1, 3, 10, 10, 10, 10, 4, 4, 10, 10, 10, 6, 6, 7, 76, 76, 104, 104, 104, 104, 104, 21, 21, 4, 4, 4, 4] 201 rigid atoms, others: [3, 4, 5, 6, 15, 16, 17, 18] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 19, 20, 21, 22, 23, 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: 478 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312583 none C#CCCN1C(NC2=NN(CCC)C=C2)=NN=C1C1=CC=C(C2=N[N-]N=N2)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.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: [1, 1, 5, 5, 8, 1, 8, 1, 8, 8, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 4, 4, 4, 4, 18, 52, 52, 52, 121, 135, 52, 52, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 20, 20, 20, 12, 12, 18, 121, 121, 135, 135, 135, 135, 135, 52, 52, 1, 1, 1, 1] 201 rigid atoms, others: [44, 45, 46, 47, 17, 18, 19, 20, 21, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 568 number of broken/clashed sets: 24 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312583 none C#CCCN1C(NC2=NN(CCC)C=C2)=NN=C1C1=CC=C(C2=N[N-]N=N2)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.pl3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.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: [1, 1, 5, 5, 8, 1, 8, 1, 8, 8, 5, 5, 5, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 40, 21, 21, 7, 1, 1, 1, 1, 1, 9, 17, 1, 1, 21, 21, 21, 21, 52, 52, 37, 37, 83, 83, 83, 83, 52, 52, 63, 63, 63, 40, 40, 7, 9, 9, 17, 17, 17, 17, 17, 1, 1, 52, 52, 52, 52] 201 rigid atoms, others: [6, 7, 8, 9, 10, 43, 13, 14, 42] set([0, 1, 2, 3, 4, 5, 11, 12, 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, 44, 45, 46, 47]) total number of confs: 504 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312583 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312583 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312583/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312583/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312583 Building REAL300020312584 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312584' /scratch/stefan/7770667/working/building/REAL300020312584 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312584 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312584/0 /scratch/stefan/7770667/working/building/REAL300020312584 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/111 `/scratch/stefan/7770667/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(C2=NOCC2)CC1) `REAL300020312584.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312584 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(C2=NOCC2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 8, 12, 5, 5, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 79, 36, 36, 36, 36, 108, 131, 142, 142, 142, 142, 36, 36, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 13, 13, 105, 105, 105, 79, 79, 108, 108, 131, 131, 13, 13, 13, 13, 13, 1, 1, 1, 1, 13, 13, 13, 13] 177 rigid atoms, others: [41, 42, 43, 44, 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, 45, 46, 47, 48]) total number of confs: 873 number of broken/clashed sets: 12 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312584 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(C2=NOCC2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 8, 12, 5, 5, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 4, 4, 4, 4, 36, 36, 36, 36, 4, 4, 11, 11, 11, 5, 5, 5, 5, 9, 9, 4, 4, 4, 4, 4, 36, 36, 36, 36, 4, 4, 4, 4] 177 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 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: 138 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312584 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(C2=NOCC2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 8, 12, 5, 5, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 11, 4, 4, 4, 4, 16, 25, 41, 41, 41, 41, 4, 4, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 1, 21, 21, 21, 11, 11, 16, 16, 25, 25, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 1, 1, 1] 177 rigid atoms, others: [48, 36, 37, 38, 39, 40, 45, 46, 15, 16, 17, 18, 19, 20, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44]) total number of confs: 233 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312584 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(C2=NOCC2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 8, 12, 5, 5, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 49, 19, 19, 8, 4, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 43, 43, 43, 43, 142, 142, 142, 142, 43, 43, 70, 70, 70, 49, 49, 8, 8, 4, 4, 43, 43, 43, 43, 43, 142, 142, 142, 142, 43, 43, 43, 43] 177 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 484 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312584 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312584/1 /scratch/stefan/7770667/working/building/REAL300020312584 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/112 `/scratch/stefan/7770667/working/3D/112' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(C2=NOCC2)CC1) `REAL300020312584.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312584 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(C2=NOCC2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 8, 12, 5, 5, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 80, 36, 36, 36, 36, 109, 132, 140, 140, 140, 140, 36, 36, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 13, 13, 107, 107, 107, 80, 80, 109, 109, 132, 132, 13, 13, 13, 13, 13, 1, 1, 1, 1, 13, 13, 13, 13] 177 rigid atoms, others: [41, 42, 43, 44, 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, 45, 46, 47, 48]) total number of confs: 885 number of broken/clashed sets: 12 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312584 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(C2=NOCC2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 8, 12, 5, 5, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 4, 4, 4, 4, 36, 36, 36, 36, 4, 4, 11, 11, 11, 5, 5, 5, 5, 9, 9, 4, 4, 4, 4, 4, 36, 36, 36, 36, 4, 4, 4, 4] 177 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 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: 138 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312584 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(C2=NOCC2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 8, 12, 5, 5, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 11, 4, 4, 4, 4, 16, 25, 41, 41, 41, 41, 4, 4, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 1, 21, 21, 21, 11, 11, 16, 16, 25, 25, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 1, 1, 1] 177 rigid atoms, others: [48, 36, 37, 38, 39, 40, 45, 46, 15, 16, 17, 18, 19, 20, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44]) total number of confs: 233 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312584 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(C2=NOCC2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 8, 12, 5, 5, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 48, 19, 19, 8, 4, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 44, 44, 44, 44, 141, 141, 141, 141, 44, 44, 68, 68, 68, 48, 48, 8, 8, 4, 4, 44, 44, 44, 44, 44, 141, 141, 141, 141, 44, 44, 44, 44] 179 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 473 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312584 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312584 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312584/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312584/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312584 Building REAL300020312585 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312585' /scratch/stefan/7770667/working/building/REAL300020312585 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312585 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312585/0 /scratch/stefan/7770667/working/building/REAL300020312585 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/113 `/scratch/stefan/7770667/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(C2=NOCC2)CC1) `REAL300020312585.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312585 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(C2=NOCC2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 8, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 62, 30, 30, 30, 30, 61, 73, 73, 73, 73, 30, 30, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 13, 13, 81, 81, 81, 62, 62, 61, 61, 13, 13, 13, 13, 13, 1, 1, 1, 1, 13, 13, 13, 13] 103 rigid atoms, others: [38, 39, 40, 41, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45]) total number of confs: 484 number of broken/clashed sets: 6 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312585 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(C2=NOCC2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 8, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 6, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 5, 5, 5, 5, 30, 30, 30, 30, 5, 5, 12, 12, 12, 6, 6, 6, 6, 5, 5, 5, 5, 5, 30, 30, 30, 30, 5, 5, 5, 5] 103 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 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: 104 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312585 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(C2=NOCC2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 8, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 13, 5, 5, 5, 5, 16, 22, 22, 22, 22, 5, 5, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 1, 19, 19, 19, 13, 13, 16, 16, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 1, 1, 1] 103 rigid atoms, others: [33, 34, 35, 36, 37, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41]) total number of confs: 136 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312585 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(C2=NOCC2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 8, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 24, 8, 8, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 22, 22, 22, 22, 73, 73, 73, 73, 22, 22, 37, 37, 37, 24, 24, 3, 3, 22, 22, 22, 22, 22, 73, 73, 73, 73, 22, 22, 22, 22] 103 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 238 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312585 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312585/1 /scratch/stefan/7770667/working/building/REAL300020312585 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/114 `/scratch/stefan/7770667/working/3D/114' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(C2=NOCC2)CC1) `REAL300020312585.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312585/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312585 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(C2=NOCC2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 8, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 61, 31, 31, 31, 31, 59, 71, 71, 71, 71, 31, 31, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 13, 13, 80, 80, 80, 61, 61, 59, 59, 13, 13, 13, 13, 13, 1, 1, 1, 1, 13, 13, 13, 13] 101 rigid atoms, others: [38, 39, 40, 41, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45]) total number of confs: 455 number of broken/clashed sets: 5 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312585 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(C2=NOCC2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 8, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 6, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 5, 5, 5, 5, 31, 31, 31, 31, 5, 5, 12, 12, 12, 6, 6, 6, 6, 5, 5, 5, 5, 5, 31, 31, 31, 31, 5, 5, 5, 5] 101 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 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: 105 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312585 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(C2=NOCC2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 8, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 13, 5, 5, 5, 5, 16, 22, 22, 22, 22, 5, 5, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 1, 19, 19, 19, 13, 13, 16, 16, 1, 1, 1, 1, 1, 13, 13, 13, 13, 1, 1, 1, 1] 101 rigid atoms, others: [33, 34, 35, 36, 37, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41]) total number of confs: 136 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312585 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(C2=NOCC2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 1, 8, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [36, 36, 23, 8, 8, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 22, 22, 22, 22, 71, 71, 71, 71, 22, 22, 36, 36, 36, 23, 23, 3, 3, 22, 22, 22, 22, 22, 71, 71, 71, 71, 22, 22, 22, 22] 101 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 233 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312585 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312585 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312585/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312585/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312585 Building REAL300020312586 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312586' /scratch/stefan/7770667/working/building/REAL300020312586 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312586 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312586/0 /scratch/stefan/7770667/working/building/REAL300020312586 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/115 `/scratch/stefan/7770667/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1C[C@@H]2C[C@H]1[C@H]1C[C@H]12) `REAL300020312586.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312586 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1C[C@@H]2C[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 7, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 8, 4, 1, 1, 1, 1, 5, 9, 15, 15, 15, 15, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 4, 4, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5] 51 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 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: 90 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312586 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1C[C@@H]2C[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 7, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 16, 10, 5, 5, 5, 5, 15, 21, 32, 32, 32, 32, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 10, 10, 15, 15, 21, 21, 1, 1, 1, 1, 1, 1] 51 rigid atoms, others: [37, 38, 39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 163 number of broken/clashed sets: 51 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312586 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1C[C@@H]2C[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 7, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 11, 7, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 15, 15, 15, 15, 15, 7, 7, 4, 4, 11, 11, 11, 11, 11, 11] 15 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 58 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312586 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312586/1 /scratch/stefan/7770667/working/building/REAL300020312586 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/116 `/scratch/stefan/7770667/working/3D/116' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1C[C@@H]2C[C@H]1[C@H]1C[C@H]12) `REAL300020312586.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312586/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312586 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1C[C@@H]2C[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 7, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 8, 4, 1, 1, 1, 1, 5, 9, 15, 15, 15, 15, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 4, 4, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5] 52 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 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: 90 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312586 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1C[C@@H]2C[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 7, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 16, 10, 5, 5, 5, 5, 15, 21, 32, 32, 32, 32, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 10, 10, 15, 15, 21, 21, 1, 1, 1, 1, 1, 1] 52 rigid atoms, others: [37, 38, 39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 163 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312586 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1C[C@@H]2C[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 7, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 11, 7, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 15, 15, 15, 15, 15, 7, 7, 4, 4, 11, 11, 11, 11, 11, 11] 15 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 58 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312586 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312586 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312586/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312586/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312586 Building REAL300020312587 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312587' /scratch/stefan/7770667/working/building/REAL300020312587 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312587 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312587/0 /scratch/stefan/7770667/working/building/REAL300020312587 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/117 `/scratch/stefan/7770667/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1C[C@@H]2C[C@H]1[C@H]1C[C@H]12) `REAL300020312587.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312587 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1C[C@@H]2C[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 7, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 4, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 6, 6, 4, 4, 4, 4, 4, 4] 26 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 60 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312587 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1C[C@@H]2C[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 7, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 6, 4, 4, 4, 4, 9, 12, 12, 12, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 6, 6, 9, 9, 1, 1, 1, 1, 1, 1] 26 rigid atoms, others: [34, 35, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 33, 27, 28, 29, 30, 31]) total number of confs: 68 number of broken/clashed sets: 26 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312587 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1C[C@@H]2C[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 7, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 17, 8, 8, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 25, 25, 25, 17, 17, 3, 3, 12, 12, 12, 12, 12, 12] 26 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 110 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312587 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312587/1 /scratch/stefan/7770667/working/building/REAL300020312587 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/118 `/scratch/stefan/7770667/working/3D/118' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1C[C@@H]2C[C@H]1[C@H]1C[C@H]12) `REAL300020312587.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312587/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312587 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1C[C@@H]2C[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 7, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 4, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 4, 4, 6, 6, 4, 4, 4, 4, 4, 4] 26 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 60 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312587 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1C[C@@H]2C[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 7, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 6, 4, 4, 4, 4, 9, 12, 12, 12, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 6, 6, 9, 9, 1, 1, 1, 1, 1, 1] 26 rigid atoms, others: [34, 35, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 33, 27, 28, 29, 30, 31]) total number of confs: 68 number of broken/clashed sets: 26 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312587 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1C[C@@H]2C[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 7, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 17, 8, 8, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 25, 25, 25, 17, 17, 3, 3, 12, 12, 12, 12, 12, 12] 26 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 110 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312587 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312587 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312587/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312587/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312587 Building REAL300020312588 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312588' /scratch/stefan/7770667/working/building/REAL300020312588 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312588 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312588/0 /scratch/stefan/7770667/working/building/REAL300020312588 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/119 `/scratch/stefan/7770667/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1C[C@@H]2C[C@H]1[C@H]1C[C@H]12) `REAL300020312588.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312588 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1C[C@@H]2C[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', '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, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 7, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 10, 5, 5, 5, 5, 9, 9, 7, 7, 10, 10, 10, 10, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 10, 10, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 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]) total number of confs: 59 number of broken/clashed sets: 17 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312588 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1C[C@@H]2C[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', '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, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 7, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 1, 1, 1, 1, 4, 4, 3, 3, 7, 7, 7, 7, 4, 4, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 7, 7, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5] 17 rigid atoms, others: [3, 4, 5, 6, 17, 18, 19, 20] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 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: 61 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312588 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1C[C@@H]2C[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', '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, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 7, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 16, 13, 7, 7, 2, 2, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 16, 16, 16, 13, 13, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10] 17 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 63 number of broken/clashed sets: 17 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312588 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1C[C@@H]2C[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', '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, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 7, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 16, 12, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 16, 16, 16, 12, 12, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9] 17 rigid atoms, others: [37, 6, 7, 8, 9, 10, 39, 15, 16, 40, 38, 5] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46]) total number of confs: 73 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312588 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312588/1 /scratch/stefan/7770667/working/building/REAL300020312588 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/120 `/scratch/stefan/7770667/working/3D/120' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1C[C@@H]2C[C@H]1[C@H]1C[C@H]12) `REAL300020312588.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312588/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312588 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1C[C@@H]2C[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', '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, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 7, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 10, 5, 5, 5, 5, 9, 9, 7, 7, 10, 10, 10, 10, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 10, 10, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 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]) total number of confs: 59 number of broken/clashed sets: 17 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312588 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1C[C@@H]2C[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', '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, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 7, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 1, 1, 1, 1, 4, 4, 3, 3, 7, 7, 7, 7, 4, 4, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 7, 7, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5] 17 rigid atoms, others: [3, 4, 5, 6, 17, 18, 19, 20] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 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: 61 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312588 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1C[C@@H]2C[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', '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, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 7, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 16, 13, 7, 7, 2, 1, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 16, 16, 16, 13, 13, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10] 17 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 66 number of broken/clashed sets: 17 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312588 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1C[C@@H]2C[C@H]1[C@H]1C[C@H]12 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', '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, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 7, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 16, 12, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 16, 16, 16, 12, 12, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9] 17 rigid atoms, others: [37, 6, 7, 8, 9, 10, 39, 15, 16, 40, 38, 5] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46]) total number of confs: 73 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312588 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312588 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312588/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312588/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312588 Building REAL300020312589 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312589' /scratch/stefan/7770667/working/building/REAL300020312589 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312589 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312589/0 /scratch/stefan/7770667/working/building/REAL300020312589 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/121 `/scratch/stefan/7770667/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC2=CC=CC=C2C2CC1C2) `REAL300020312589.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312589 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC2=CC=CC=C2C2CC1C2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 10, 5, 1, 1, 1, 1, 5, 9, 13, 13, 13, 13, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 5, 5, 5, 5, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 39 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 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: 94 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312589 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC2=CC=CC=C2C2CC1C2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 15, 9, 4, 4, 4, 4, 12, 17, 21, 21, 21, 21, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 9, 9, 12, 12, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 39 rigid atoms, others: [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] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 133 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312589 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC2=CC=CC=C2C2CC1C2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 8, 8, 5, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 5, 5, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 9 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 29 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312589 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312589/1 /scratch/stefan/7770667/working/building/REAL300020312589 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/122 `/scratch/stefan/7770667/working/3D/122' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC2=CC=CC=C2C2CC1C2) `REAL300020312589.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312589/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312589 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC2=CC=CC=C2C2CC1C2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 10, 5, 1, 1, 1, 1, 5, 9, 13, 13, 13, 13, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 5, 5, 5, 5, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 39 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 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: 94 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312589 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC2=CC=CC=C2C2CC1C2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 15, 9, 4, 4, 4, 4, 12, 17, 21, 21, 21, 21, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 9, 9, 12, 12, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 39 rigid atoms, others: [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] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 133 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312589 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC2=CC=CC=C2C2CC1C2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 8, 8, 5, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 5, 5, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 9 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 29 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312589 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312589 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312589/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312589/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312589 Building REAL300020312590 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312590' /scratch/stefan/7770667/working/building/REAL300020312590 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312590 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312590/0 /scratch/stefan/7770667/working/building/REAL300020312590 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/123 `/scratch/stefan/7770667/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC2=CC=CC=C2C2CC1C2) `REAL300020312590.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312590 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC2=CC=CC=C2C2CC1C2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 5, 1, 1, 1, 1, 4, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 5, 5, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 35 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312590 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC2=CC=CC=C2C2CC1C2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 11, 6, 6, 6, 6, 16, 20, 20, 20, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 11, 11, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 35 rigid atoms, others: [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] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 33, 27, 28, 29, 30, 31]) total number of confs: 117 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312590 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC2=CC=CC=C2C2CC1C2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 17, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 20, 20, 20, 17, 17, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 35 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 103 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312590 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312590/1 /scratch/stefan/7770667/working/building/REAL300020312590 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/124 `/scratch/stefan/7770667/working/3D/124' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC2=CC=CC=C2C2CC1C2) `REAL300020312590.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312590/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312590 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC2=CC=CC=C2C2CC1C2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 5, 1, 1, 1, 1, 4, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 5, 5, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 35 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312590 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC2=CC=CC=C2C2CC1C2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 11, 6, 6, 6, 6, 16, 20, 20, 20, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 11, 11, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 35 rigid atoms, others: [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] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 33, 27, 28, 29, 30, 31]) total number of confs: 117 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312590 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC2=CC=CC=C2C2CC1C2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 17, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 20, 20, 20, 17, 17, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 35 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 102 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312590 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312590 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312590/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312590/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312590 Building REAL300020312591 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312591' /scratch/stefan/7770667/working/building/REAL300020312591 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312591 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312591/0 /scratch/stefan/7770667/working/building/REAL300020312591 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/125 `/scratch/stefan/7770667/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(C1)CC=CCO2) `REAL300020312591.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312591 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(C1)CC=CCO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 1, 5, 12, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 6, 1, 1, 1, 1, 6, 10, 17, 17, 17, 17, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 6, 6, 6, 6, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 79 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 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: 111 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312591 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(C1)CC=CCO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 1, 5, 12, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 18, 6, 6, 6, 6, 24, 37, 49, 49, 49, 49, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 18, 18, 24, 24, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 79 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 304 number of broken/clashed sets: 11 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312591 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(C1)CC=CCO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 1, 5, 12, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 16, 16, 8, 4, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 25, 25, 25, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 8, 8, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 32 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 112 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312591 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312591/1 /scratch/stefan/7770667/working/building/REAL300020312591 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/126 `/scratch/stefan/7770667/working/3D/126' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(C1)CC=CCO2) `REAL300020312591.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312591/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312591 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(C1)CC=CCO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 1, 5, 12, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 6, 1, 1, 1, 1, 6, 10, 17, 17, 17, 17, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 6, 6, 6, 6, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 80 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 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: 111 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312591 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(C1)CC=CCO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 1, 5, 12, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 18, 6, 6, 6, 6, 24, 37, 49, 49, 49, 49, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 18, 18, 24, 24, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 80 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 304 number of broken/clashed sets: 11 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312591 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(C1)CC=CCO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 1, 5, 12, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 16, 16, 8, 4, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 25, 25, 25, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 8, 8, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 32 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 112 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312591 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312591 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312591/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312591/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312591 Building REAL300020312592 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312592' /scratch/stefan/7770667/working/building/REAL300020312592 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312592 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312592/0 /scratch/stefan/7770667/working/building/REAL300020312592 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/127 `/scratch/stefan/7770667/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(C1)CC=CCO2) `REAL300020312592.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312592 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(C1)CC=CCO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 1, 5, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 43 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 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: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312592 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(C1)CC=CCO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 1, 5, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 17, 6, 6, 6, 6, 17, 25, 25, 25, 25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 43 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312592 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(C1)CC=CCO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 1, 5, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 20, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 25, 25, 25, 25, 25, 25, 25, 25, 25, 29, 29, 29, 20, 20, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 43 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 144 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312592 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312592/1 /scratch/stefan/7770667/working/building/REAL300020312592 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/128 `/scratch/stefan/7770667/working/3D/128' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(C1)CC=CCO2) `REAL300020312592.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312592/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312592 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(C1)CC=CCO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 1, 5, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 43 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 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: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312592 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(C1)CC=CCO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 1, 5, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 17, 6, 6, 6, 6, 17, 25, 25, 25, 25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 43 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312592 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(C1)CC=CCO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 1, 5, 12, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 20, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 25, 25, 25, 25, 25, 25, 25, 25, 25, 29, 29, 29, 20, 20, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 43 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 144 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312592 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312592 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312592/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312592/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312592 Building REAL300020312593 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312593' /scratch/stefan/7770667/working/building/REAL300020312593 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312593 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312593/0 /scratch/stefan/7770667/working/building/REAL300020312593 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/129 `/scratch/stefan/7770667/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCOCCOCC1) `REAL300020312593.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312593 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCOCCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 12, 5, 5, 12, 5, 5, 7, 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, 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, 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: [11, 11, 5, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 5, 5, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 60 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 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: 104 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312593 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCOCCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 12, 5, 5, 12, 5, 5, 7, 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, 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, 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: [23, 23, 12, 5, 5, 5, 5, 18, 29, 38, 38, 38, 38, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 12, 12, 18, 18, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 60 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 231 number of broken/clashed sets: 60 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312593 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCOCCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 12, 5, 5, 12, 5, 5, 7, 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, 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, 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: [19, 19, 18, 12, 12, 8, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 18, 19, 19, 19, 18, 18, 8, 8, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 21 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 86 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312593 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312593/1 /scratch/stefan/7770667/working/building/REAL300020312593 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/130 `/scratch/stefan/7770667/working/3D/130' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCOCCOCC1) `REAL300020312593.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312593/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312593 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCOCCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 12, 5, 5, 12, 5, 5, 7, 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, 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, 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: [11, 11, 5, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 5, 5, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 60 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 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: 104 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312593 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCOCCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 12, 5, 5, 12, 5, 5, 7, 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, 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, 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: [23, 23, 12, 5, 5, 5, 5, 18, 29, 38, 38, 38, 38, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 12, 12, 18, 18, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 60 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 231 number of broken/clashed sets: 60 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312593 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCOCCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 12, 5, 5, 12, 5, 5, 7, 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, 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, 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: [19, 19, 18, 12, 12, 8, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 18, 18, 18, 18, 18, 18, 18, 18, 19, 19, 19, 18, 18, 8, 8, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 21 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 86 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312593 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312593 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312593/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312593/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312593 Building REAL300020312594 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312594' /scratch/stefan/7770667/working/building/REAL300020312594 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312594 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312594/0 /scratch/stefan/7770667/working/building/REAL300020312594 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/131 `/scratch/stefan/7770667/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCOCCOCC1) `REAL300020312594.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312594 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCOCCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 12, 5, 5, 12, 5, 5, 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, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 5, 5, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 41 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 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: 70 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312594 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCOCCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 12, 5, 5, 12, 5, 5, 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, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 11, 5, 5, 5, 5, 15, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 11, 11, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 41 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 120 number of broken/clashed sets: 41 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312594 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCOCCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 12, 5, 5, 12, 5, 5, 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, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 23, 8, 8, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 35, 35, 35, 23, 23, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 41 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 167 number of broken/clashed sets: 41 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312594 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312594/1 /scratch/stefan/7770667/working/building/REAL300020312594 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/132 `/scratch/stefan/7770667/working/3D/132' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCOCCOCC1) `REAL300020312594.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312594 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCOCCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 12, 5, 5, 12, 5, 5, 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, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 5, 5, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 41 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 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: 70 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312594 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCOCCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 12, 5, 5, 12, 5, 5, 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, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 11, 5, 5, 5, 5, 15, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 11, 11, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 41 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 120 number of broken/clashed sets: 41 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312594 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCOCCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 12, 5, 5, 12, 5, 5, 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, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 23, 8, 8, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 21, 21, 21, 21, 21, 21, 21, 21, 35, 35, 35, 23, 23, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 41 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 167 number of broken/clashed sets: 41 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312594 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312594 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312594/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312594/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312594 Building REAL300020312595 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312595' /scratch/stefan/7770667/working/building/REAL300020312595 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312595 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312595/0 /scratch/stefan/7770667/working/building/REAL300020312595 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/133 `/scratch/stefan/7770667/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CCOCCOCC1) `REAL300020312595.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312595 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CCOCCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 12, 5, 5, 7, 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, 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, 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: [21, 21, 15, 5, 5, 5, 5, 10, 10, 5, 5, 12, 12, 12, 12, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 15, 15, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 24 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49] set([0, 1, 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]) total number of confs: 117 number of broken/clashed sets: 24 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312595 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CCOCCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 12, 5, 5, 7, 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, 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, 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: [14, 14, 7, 1, 1, 1, 1, 4, 4, 1, 1, 6, 6, 6, 6, 4, 4, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 7, 7, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 24 rigid atoms, others: [3, 4, 5, 6, 17, 18, 19, 20] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 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: 81 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312595 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CCOCCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 12, 5, 5, 7, 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, 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, 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: [21, 21, 14, 6, 6, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 21, 21, 21, 14, 14, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 24 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 94 number of broken/clashed sets: 24 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312595 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CCOCCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 12, 5, 5, 7, 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, 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, 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: [20, 20, 12, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 20, 20, 20, 12, 12, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 24 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 15, 16, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 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: 93 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312595 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312595/1 /scratch/stefan/7770667/working/building/REAL300020312595 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/134 `/scratch/stefan/7770667/working/3D/134' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CCOCCOCC1) `REAL300020312595.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312595/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312595 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CCOCCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 12, 5, 5, 7, 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, 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, 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: [21, 21, 15, 5, 5, 5, 5, 10, 10, 9, 9, 12, 12, 12, 12, 10, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 15, 15, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 24 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49] set([0, 1, 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]) total number of confs: 102 number of broken/clashed sets: 24 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312595 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CCOCCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 12, 5, 5, 7, 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, 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, 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: [14, 14, 7, 1, 1, 1, 1, 4, 4, 3, 3, 6, 6, 6, 6, 4, 4, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 7, 7, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 24 rigid atoms, others: [3, 4, 5, 6, 17, 18, 19, 20] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 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: 78 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312595 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CCOCCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 12, 5, 5, 7, 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, 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, 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: [21, 21, 14, 6, 6, 2, 1, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 21, 21, 21, 14, 14, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12] 24 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 96 number of broken/clashed sets: 24 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312595 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CCOCCOCC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'O.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 12, 5, 5, 12, 5, 5, 7, 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, 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, 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: [20, 20, 12, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 4, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 20, 20, 20, 12, 12, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 24 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 15, 16, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 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: 93 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312595 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312595 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312595/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312595/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312595 Building REAL300020312596 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312596' /scratch/stefan/7770667/working/building/REAL300020312596 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312596 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312596/0 /scratch/stefan/7770667/working/building/REAL300020312596 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/135 `/scratch/stefan/7770667/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCCCC2(CCOCC2)C1) `REAL300020312596.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312596 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCCCC2(CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 4, 1, 1, 1, 1, 5, 9, 10, 10, 10, 10, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 4, 4, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 36 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 77 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312596 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCCCC2(CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 9, 5, 5, 5, 5, 17, 27, 28, 28, 28, 28, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 9, 9, 17, 17, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 36 rigid atoms, others: [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, 49, 50, 51, 52, 53, 54] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 161 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312596 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCCCC2(CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 13, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 14, 14, 14, 13, 13, 4, 4, 2, 2, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 16 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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, 54]) total number of confs: 71 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312596 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312596/1 /scratch/stefan/7770667/working/building/REAL300020312596 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/136 `/scratch/stefan/7770667/working/3D/136' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCCCC2(CCOCC2)C1) `REAL300020312596.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312596/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312596 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCCCC2(CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 4, 1, 1, 1, 1, 5, 9, 10, 10, 10, 10, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 4, 4, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 36 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 77 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312596 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCCCC2(CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 9, 5, 5, 5, 5, 17, 27, 28, 28, 28, 28, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 9, 9, 17, 17, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 36 rigid atoms, others: [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, 49, 50, 51, 52, 53, 54] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 161 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312596 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCCCC2(CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 13, 8, 8, 4, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 14, 14, 14, 13, 13, 4, 4, 2, 2, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 16 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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, 54]) total number of confs: 71 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312596 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312596 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312596/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312596/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312596 Building REAL300020312597 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312597' /scratch/stefan/7770667/working/building/REAL300020312597 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312597 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312597/0 /scratch/stefan/7770667/working/building/REAL300020312597 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/137 `/scratch/stefan/7770667/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCCCC2(CCOCC2)C1) `REAL300020312597.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312597 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCCCC2(CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 3, 1, 1, 1, 1, 5, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 3, 3, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 11 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: 43 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312597 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCCCC2(CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 4, 4, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 11 rigid atoms, others: [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, 50, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 33, 27, 28, 29, 30, 31]) total number of confs: 38 number of broken/clashed sets: 11 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312597 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCCCC2(CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 10, 8, 8, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 11 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 41 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312597 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312597/1 /scratch/stefan/7770667/working/building/REAL300020312597 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/138 `/scratch/stefan/7770667/working/3D/138' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCCCC2(CCOCC2)C1) `REAL300020312597.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312597 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCCCC2(CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 3, 1, 1, 1, 1, 5, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 3, 3, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 11 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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: 43 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312597 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCCCC2(CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 4, 4, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 11 rigid atoms, others: [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, 50, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 33, 27, 28, 29, 30, 31]) total number of confs: 38 number of broken/clashed sets: 11 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312597 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCCCC2(CCOCC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 10, 8, 8, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 11 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 41 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312597 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312597 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312597/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312597/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312597 Building REAL300020312598 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312598' /scratch/stefan/7770667/working/building/REAL300020312598 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312598 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312598/0 /scratch/stefan/7770667/working/building/REAL300020312598 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/139 `/scratch/stefan/7770667/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N(C)CCCNC(=O)OCCC) `REAL300020312598.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312598 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N(C)CCCNC(=O)OCCC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 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] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 7, 7, 7, 7, 1, 1, 1, 1, 4, 4, 8, 12, 19, 50, 76, 76, 76, 123, 150, 3, 3, 3, 3, 3, 5, 5, 5, 5, 4, 4, 4, 8, 8, 14, 14, 19, 19, 50, 123, 123, 150, 150, 150, 150, 150] 201 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 674 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312598 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N(C)CCCNC(=O)OCCC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 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] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 4, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 17, 17, 20, 29, 36, 88, 132, 132, 132, 197, 200, 11, 11, 11, 11, 11, 4, 4, 4, 4, 17, 17, 17, 20, 20, 29, 29, 36, 36, 88, 197, 197, 201, 201, 200, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 831 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312598 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312598/1 /scratch/stefan/7770667/working/building/REAL300020312598 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/140 `/scratch/stefan/7770667/working/3D/140' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N(C)CCCNC(=O)OCCC) `REAL300020312598.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312598/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312598 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N(C)CCCNC(=O)OCCC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 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] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 7, 7, 7, 7, 1, 1, 1, 1, 4, 4, 8, 12, 19, 50, 75, 75, 75, 122, 149, 3, 3, 3, 3, 3, 5, 5, 5, 5, 4, 4, 4, 8, 8, 14, 14, 19, 19, 50, 122, 122, 150, 150, 150, 150, 150] 201 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312598 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N(C)CCCNC(=O)OCCC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 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] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 4, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 17, 17, 20, 29, 36, 87, 132, 132, 132, 197, 201, 11, 11, 11, 11, 11, 4, 4, 4, 4, 17, 17, 17, 20, 20, 29, 29, 36, 36, 87, 197, 197, 201, 201, 201, 201, 201] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 828 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312598 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312598 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312598/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312598/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312598 Building REAL300020312599 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312599' /scratch/stefan/7770667/working/building/REAL300020312599 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312599 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312599/0 /scratch/stefan/7770667/working/building/REAL300020312599 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/141 `/scratch/stefan/7770667/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(C)CCCNC(=O)OCCC) `REAL300020312599.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312599 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(C)CCCNC(=O)OCCC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 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] dock color type numbers: [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, 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: [2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4] 4 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 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: 25 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312599 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(C)CCCNC(=O)OCCC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 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] dock color type numbers: [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, 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: [2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 4, 4, 2, 2, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4] 4 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11] 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 11 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312599 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312599/1 /scratch/stefan/7770667/working/building/REAL300020312599 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/142 `/scratch/stefan/7770667/working/3D/142' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(C)CCCNC(=O)OCCC) `REAL300020312599.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312599/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312599 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(C)CCCNC(=O)OCCC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 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] dock color type numbers: [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, 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: [2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4] 4 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 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: 25 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312599 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(C)CCCNC(=O)OCCC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 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] dock color type numbers: [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, 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: [2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 4, 4, 2, 2, 2, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4] 4 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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, 46, 47, 48, 49, 50]) total number of confs: 11 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312599 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312599 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312599/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312599/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312599 Building REAL300020312600 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312600' /scratch/stefan/7770667/working/building/REAL300020312600 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312600 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312600/0 /scratch/stefan/7770667/working/building/REAL300020312600 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/143 `/scratch/stefan/7770667/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC=CCC2(CC2)C1) `REAL300020312600.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312600 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC=CCC2(CC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 9, 5, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 5, 5, 5, 5, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 61 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312600 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC=CCC2(CC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 4, 4, 4, 4, 16, 25, 36, 36, 36, 36, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 11, 11, 16, 16, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 61 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312600 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC=CCC2(CC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 24, 22, 13, 13, 8, 4, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 20, 20, 20, 20, 20, 20, 20, 20, 24, 24, 24, 22, 22, 8, 8, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 28 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312600 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312600/1 /scratch/stefan/7770667/working/building/REAL300020312600 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/144 `/scratch/stefan/7770667/working/3D/144' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC=CCC2(CC2)C1) `REAL300020312600.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312600 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC=CCC2(CC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 9, 5, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 5, 5, 5, 5, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 61 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312600 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC=CCC2(CC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 4, 4, 4, 4, 16, 25, 36, 36, 36, 36, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 11, 11, 16, 16, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 61 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312600 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC=CCC2(CC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [24, 24, 22, 13, 13, 8, 4, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 20, 20, 20, 20, 20, 20, 20, 20, 24, 24, 24, 22, 22, 8, 8, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 28 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 115 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312600 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312600 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312600/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312600/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312600 Building REAL300020312601 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312601' /scratch/stefan/7770667/working/building/REAL300020312601 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312601 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312601/0 /scratch/stefan/7770667/working/building/REAL300020312601 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/145 `/scratch/stefan/7770667/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC=CCC2(CC2)C1) `REAL300020312601.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312601 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC=CCC2(CC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 5, 5, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 37 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 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: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312601 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC=CCC2(CC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 10, 4, 4, 4, 4, 13, 19, 19, 19, 19, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 10, 10, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 37 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 110 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312601 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC=CCC2(CC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 23, 8, 8, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 33, 33, 33, 23, 23, 3, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 37 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 156 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312601 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312601/1 /scratch/stefan/7770667/working/building/REAL300020312601 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/146 `/scratch/stefan/7770667/working/3D/146' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC=CCC2(CC2)C1) `REAL300020312601.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312601/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312601 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC=CCC2(CC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 5, 5, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 37 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 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: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312601 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC=CCC2(CC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 10, 4, 4, 4, 4, 13, 19, 19, 19, 19, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 10, 10, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 37 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 110 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312601 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC=CCC2(CC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 23, 8, 8, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 33, 33, 33, 23, 23, 3, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 37 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 156 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312601 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312601 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312601/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312601/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312601 Building REAL300020312602 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312602' /scratch/stefan/7770667/working/building/REAL300020312602 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312602 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312602/0 /scratch/stefan/7770667/working/building/REAL300020312602 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/147 `/scratch/stefan/7770667/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CC=CCC2(CC2)C1) `REAL300020312602.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312602 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CC=CCC2(CC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 14, 4, 4, 4, 4, 9, 9, 4, 7, 9, 9, 9, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 14, 14, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 20 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49] set([0, 1, 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]) total number of confs: 84 number of broken/clashed sets: 4 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312602 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CC=CCC2(CC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 12, 7, 1, 1, 1, 1, 5, 5, 1, 3, 6, 6, 6, 6, 5, 5, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 7, 7, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 20 rigid atoms, others: [3, 4, 5, 6, 17, 18, 19, 20] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 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: 74 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312602 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CC=CCC2(CC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 14, 6, 6, 2, 2, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 17, 14, 14, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 20 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 74 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312602 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CC=CCC2(CC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 13, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 17, 13, 13, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 20 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 15, 16, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 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: 68 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312602 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312602/1 /scratch/stefan/7770667/working/building/REAL300020312602 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/148 `/scratch/stefan/7770667/working/3D/148' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CC=CCC2(CC2)C1) `REAL300020312602.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312602 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CC=CCC2(CC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 17, 13, 4, 4, 4, 4, 8, 8, 4, 4, 9, 9, 9, 9, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 13, 13, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 19 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49] set([0, 1, 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]) total number of confs: 90 number of broken/clashed sets: 3 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312602 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CC=CCC2(CC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [13, 13, 8, 1, 1, 1, 1, 4, 4, 1, 1, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 13, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 19 rigid atoms, others: [3, 4, 5, 6, 17, 18, 19, 20] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 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: 73 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312602 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CC=CCC2(CC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 17, 13, 5, 5, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 17, 13, 13, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 19 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 73 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312602 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CC=CCC2(CC2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 1, 1, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 17, 12, 4, 4, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 12, 12, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 19 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 15, 16, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 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: 73 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312602 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312602 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312602/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312602/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312602 Building REAL300020312603 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312603' /scratch/stefan/7770667/working/building/REAL300020312603 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312603 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312603/0 /scratch/stefan/7770667/working/building/REAL300020312603 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/149 `/scratch/stefan/7770667/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N(C)[C@@H]1C[C@H]1C1=CC=CC=C1) `REAL300020312603.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312603 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N(C)[C@@H]1C[C@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [70, 70, 53, 25, 25, 25, 25, 78, 80, 104, 104, 104, 104, 25, 25, 11, 4, 11, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 70, 70, 70, 53, 53, 78, 78, 80, 80, 11, 11, 11, 4, 4, 1, 1, 1, 1, 1] 138 rigid atoms, others: [43, 44, 45, 46, 47, 21, 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, 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: 10 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312603 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N(C)[C@@H]1C[C@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 10, 5, 1, 1, 1, 1, 5, 7, 12, 12, 12, 12, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 25, 25, 11, 25, 25, 10, 10, 10, 5, 5, 5, 5, 7, 7, 5, 5, 5, 11, 11, 25, 25, 25, 25, 25] 138 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 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: 182 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312603 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N(C)[C@@H]1C[C@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 38, 24, 11, 11, 11, 11, 42, 44, 71, 71, 71, 71, 11, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 38, 38, 38, 24, 24, 42, 42, 44, 44, 5, 5, 5, 1, 1, 4, 4, 3, 4, 4] 138 rigid atoms, others: [41, 42, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47]) total number of confs: 359 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312603 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N(C)[C@@H]1C[C@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [59, 59, 40, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 34, 34, 71, 71, 71, 71, 71, 104, 104, 75, 104, 104, 59, 59, 59, 40, 40, 6, 6, 4, 4, 34, 34, 34, 71, 71, 104, 104, 104, 104, 104] 138 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 629 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312603 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312603/1 /scratch/stefan/7770667/working/building/REAL300020312603 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/150 `/scratch/stefan/7770667/working/3D/150' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N(C)[C@@H]1C[C@H]1C1=CC=CC=C1) `REAL300020312603.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312603 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N(C)[C@@H]1C[C@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [70, 70, 53, 25, 25, 25, 25, 79, 81, 105, 105, 105, 105, 25, 25, 11, 4, 11, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 70, 70, 70, 53, 53, 79, 79, 81, 81, 11, 11, 11, 4, 4, 1, 1, 1, 1, 1] 139 rigid atoms, others: [43, 44, 45, 46, 47, 21, 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, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 577 number of broken/clashed sets: 10 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312603 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N(C)[C@@H]1C[C@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 10, 5, 1, 1, 1, 1, 5, 7, 12, 12, 12, 12, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 25, 25, 11, 25, 25, 10, 10, 10, 5, 5, 5, 5, 7, 7, 5, 5, 5, 11, 11, 25, 25, 25, 25, 25] 139 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 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: 182 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312603 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N(C)[C@@H]1C[C@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [38, 38, 24, 11, 11, 11, 11, 42, 44, 72, 72, 72, 72, 11, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 38, 38, 38, 24, 24, 42, 42, 44, 44, 5, 5, 5, 1, 1, 4, 4, 3, 4, 4] 139 rigid atoms, others: [41, 42, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47]) total number of confs: 361 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312603 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N(C)[C@@H]1C[C@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [57, 57, 39, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 33, 33, 71, 71, 71, 71, 71, 105, 105, 75, 105, 105, 57, 57, 57, 39, 39, 6, 6, 4, 4, 33, 33, 33, 71, 71, 105, 105, 105, 105, 105] 139 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 633 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312603 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312603 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312603/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312603/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312603 Building REAL300020312604 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312604' /scratch/stefan/7770667/working/building/REAL300020312604 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312604 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312604/0 /scratch/stefan/7770667/working/building/REAL300020312604 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/151 `/scratch/stefan/7770667/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(C)[C@@H]1C[C@H]1C1=CC=CC=C1) `REAL300020312604.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312604 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(C)[C@@H]1C[C@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 15, 11, 11, 11, 11, 18, 20, 20, 20, 20, 11, 11, 6, 3, 6, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 20, 20, 20, 15, 15, 18, 18, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1] 30 rigid atoms, others: [40, 41, 42, 43, 44, 20, 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, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 120 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312604 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(C)[C@@H]1C[C@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 9, 5, 1, 1, 1, 1, 3, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 11, 11, 7, 11, 11, 9, 9, 9, 5, 5, 3, 3, 4, 4, 4, 7, 7, 11, 11, 11, 11, 11] 30 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 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: 99 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312604 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(C)[C@@H]1C[C@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 7, 7, 7, 7, 12, 15, 15, 15, 15, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 17, 17, 17, 12, 12, 12, 12, 4, 4, 4, 1, 1, 3, 3, 2, 3, 3] 30 rigid atoms, others: [38, 39, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 113 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312604 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(C)[C@@H]1C[C@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 19, 12, 5, 5, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 11, 11, 15, 15, 15, 15, 15, 20, 20, 15, 20, 20, 19, 19, 19, 12, 12, 3, 3, 11, 11, 11, 15, 15, 20, 20, 20, 20, 20] 30 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 151 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312604 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312604/1 /scratch/stefan/7770667/working/building/REAL300020312604 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/152 `/scratch/stefan/7770667/working/3D/152' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(C)[C@@H]1C[C@H]1C1=CC=CC=C1) `REAL300020312604.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312604 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(C)[C@@H]1C[C@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 15, 11, 11, 11, 11, 18, 20, 20, 20, 20, 11, 11, 6, 3, 6, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 20, 20, 20, 15, 15, 18, 18, 6, 6, 6, 3, 3, 1, 1, 1, 1, 1] 30 rigid atoms, others: [40, 41, 42, 43, 44, 20, 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, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 120 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312604 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(C)[C@@H]1C[C@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 9, 5, 1, 1, 1, 1, 3, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 11, 11, 7, 11, 11, 9, 9, 9, 5, 5, 3, 3, 4, 4, 4, 7, 7, 11, 11, 11, 11, 11] 30 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 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: 99 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312604 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(C)[C@@H]1C[C@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 7, 7, 7, 7, 12, 15, 15, 15, 15, 7, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 3, 3, 1, 3, 3, 17, 17, 17, 12, 12, 12, 12, 4, 4, 4, 1, 1, 3, 3, 2, 3, 3] 30 rigid atoms, others: [38, 39, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44]) total number of confs: 113 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312604 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(C)[C@@H]1C[C@H]1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [19, 19, 12, 5, 5, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 11, 11, 15, 15, 15, 15, 15, 20, 20, 15, 20, 20, 19, 19, 19, 12, 12, 3, 3, 11, 11, 11, 15, 15, 20, 20, 20, 20, 20] 30 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 151 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312604 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312604 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312604/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312604/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312604 Building REAL300020312605 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312605' /scratch/stefan/7770667/working/building/REAL300020312605 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312605 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312605/0 /scratch/stefan/7770667/working/building/REAL300020312605 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/153 `/scratch/stefan/7770667/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N(CC1=NOC(C2CC2)=C1)C(C)C) `REAL300020312605.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312605 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N(CC1=NOC(C2CC2)=C1)C(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 8, 12, 1, 5, 5, 5, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 105, 105, 105, 105, 174, 193, 194, 194, 194, 194, 105, 105, 78, 49, 13, 12, 12, 13, 1, 1, 1, 1, 13, 78, 92, 92, 122, 122, 122, 122, 122, 174, 174, 193, 193, 49, 49, 1, 1, 1, 1, 1, 13, 92, 92, 92, 92, 92, 92, 92] 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 936 number of broken/clashed sets: 114 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312605 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N(CC1=NOC(C2CC2)=C1)C(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 8, 12, 1, 5, 5, 5, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 5, 7, 12, 12, 12, 12, 1, 1, 1, 1, 4, 12, 28, 28, 28, 28, 105, 105, 28, 4, 8, 8, 7, 7, 7, 5, 5, 5, 5, 7, 7, 12, 12, 105, 105, 105, 105, 105, 28, 8, 8, 8, 8, 8, 8, 8] 201 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 347 number of broken/clashed sets: 114 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312605 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N(CC1=NOC(C2CC2)=C1)C(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 8, 12, 1, 5, 5, 5, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 41, 28, 28, 28, 28, 85, 102, 122, 122, 122, 122, 28, 28, 17, 8, 1, 1, 1, 1, 1, 1, 13, 13, 1, 17, 27, 27, 43, 43, 43, 41, 41, 85, 85, 102, 102, 8, 8, 13, 13, 13, 13, 13, 1, 27, 27, 27, 27, 27, 27, 27] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 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: 606 number of broken/clashed sets: 114 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312605 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N(CC1=NOC(C2CC2)=C1)C(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 8, 12, 1, 5, 5, 5, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 26, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 33, 75, 123, 123, 123, 123, 194, 194, 123, 33, 48, 48, 28, 28, 28, 26, 26, 6, 6, 4, 4, 75, 75, 194, 194, 194, 194, 194, 123, 48, 48, 48, 48, 48, 48, 48] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 778 number of broken/clashed sets: 114 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312605 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312605/1 /scratch/stefan/7770667/working/building/REAL300020312605 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/154 `/scratch/stefan/7770667/working/3D/154' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N(CC1=NOC(C2CC2)=C1)C(C)C) `REAL300020312605.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312605/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312605 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N(CC1=NOC(C2CC2)=C1)C(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 8, 12, 1, 5, 5, 5, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 107, 107, 107, 107, 175, 194, 195, 195, 195, 195, 107, 107, 78, 49, 13, 12, 12, 13, 1, 1, 1, 1, 13, 78, 93, 93, 123, 123, 123, 123, 123, 175, 175, 194, 194, 49, 49, 1, 1, 1, 1, 1, 13, 93, 93, 93, 93, 93, 93, 93] 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, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 937 number of broken/clashed sets: 113 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312605 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N(CC1=NOC(C2CC2)=C1)C(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 8, 12, 1, 5, 5, 5, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 5, 1, 1, 1, 1, 5, 7, 12, 12, 12, 12, 1, 1, 1, 1, 4, 12, 28, 28, 28, 28, 107, 107, 28, 4, 8, 8, 7, 7, 7, 5, 5, 5, 5, 7, 7, 12, 12, 107, 107, 107, 107, 107, 28, 8, 8, 8, 8, 8, 8, 8] 201 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 351 number of broken/clashed sets: 113 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312605 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N(CC1=NOC(C2CC2)=C1)C(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 8, 12, 1, 5, 5, 5, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 41, 28, 28, 28, 28, 87, 104, 125, 125, 125, 125, 28, 28, 17, 8, 1, 1, 1, 1, 1, 1, 13, 13, 1, 17, 28, 28, 43, 43, 43, 41, 41, 87, 87, 104, 104, 8, 8, 13, 13, 13, 13, 13, 1, 28, 28, 28, 28, 28, 28, 28] 201 rigid atoms, others: [45, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 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: 620 number of broken/clashed sets: 113 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312605 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N(CC1=NOC(C2CC2)=C1)C(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', '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', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 8, 12, 1, 5, 5, 5, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7] 0 hydrogens 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, 26, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 33, 76, 124, 124, 124, 124, 195, 195, 124, 33, 50, 50, 28, 28, 28, 26, 26, 6, 6, 4, 4, 76, 76, 195, 195, 195, 195, 195, 124, 50, 50, 50, 50, 50, 50, 50] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 797 number of broken/clashed sets: 113 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312605 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312605 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312605/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312605/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312605 Building REAL300020312606 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312606' /scratch/stefan/7770667/working/building/REAL300020312606 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312606 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312606/0 /scratch/stefan/7770667/working/building/REAL300020312606 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/155 `/scratch/stefan/7770667/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(CC1=NOC(C2CC2)=C1)C(C)C) `REAL300020312606.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312606 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(CC1=NOC(C2CC2)=C1)C(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 8, 12, 1, 5, 5, 5, 1, 5, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [149, 149, 149, 111, 111, 111, 111, 138, 163, 163, 163, 163, 111, 111, 78, 48, 13, 12, 12, 13, 1, 1, 1, 1, 13, 78, 111, 111, 149, 149, 149, 149, 149, 138, 138, 48, 48, 1, 1, 1, 1, 1, 13, 111, 111, 111, 111, 111, 111, 111] 201 rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 897 number of broken/clashed sets: 116 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312606 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(CC1=NOC(C2CC2)=C1)C(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 8, 12, 1, 5, 5, 5, 1, 5, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 7, 5, 1, 1, 1, 1, 3, 5, 5, 5, 5, 1, 1, 1, 1, 4, 15, 36, 36, 36, 36, 112, 112, 36, 4, 11, 11, 7, 7, 7, 5, 5, 3, 3, 15, 15, 112, 112, 112, 112, 112, 36, 11, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 355 number of broken/clashed sets: 114 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312606 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(CC1=NOC(C2CC2)=C1)C(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 8, 12, 1, 5, 5, 5, 1, 5, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [58, 58, 54, 36, 36, 36, 36, 51, 80, 80, 80, 80, 36, 36, 19, 9, 1, 1, 1, 1, 1, 1, 13, 13, 1, 19, 38, 38, 58, 58, 58, 54, 54, 51, 51, 9, 9, 13, 13, 13, 13, 13, 1, 38, 38, 38, 38, 38, 38, 38] 201 rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 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: 463 number of broken/clashed sets: 115 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312606 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(CC1=NOC(C2CC2)=C1)C(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 8, 12, 1, 5, 5, 5, 1, 5, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [21, 21, 19, 8, 8, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 20, 52, 85, 85, 85, 85, 169, 169, 85, 20, 36, 36, 21, 21, 21, 19, 19, 4, 4, 52, 52, 169, 169, 169, 169, 169, 85, 36, 36, 36, 36, 36, 36, 36] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 651 number of broken/clashed sets: 116 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312606 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312606/1 /scratch/stefan/7770667/working/building/REAL300020312606 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/156 `/scratch/stefan/7770667/working/3D/156' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(CC1=NOC(C2CC2)=C1)C(C)C) `REAL300020312606.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312606/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312606 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(CC1=NOC(C2CC2)=C1)C(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 8, 12, 1, 5, 5, 5, 1, 5, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [151, 151, 151, 113, 113, 113, 113, 138, 163, 163, 163, 163, 113, 113, 79, 48, 12, 11, 11, 12, 1, 1, 1, 1, 12, 79, 112, 112, 151, 151, 151, 151, 151, 138, 138, 48, 48, 1, 1, 1, 1, 1, 12, 112, 112, 112, 112, 112, 112, 112] 201 rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 884 number of broken/clashed sets: 117 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312606 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(CC1=NOC(C2CC2)=C1)C(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 8, 12, 1, 5, 5, 5, 1, 5, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 7, 5, 1, 1, 1, 1, 3, 5, 5, 5, 5, 1, 1, 1, 1, 4, 15, 36, 36, 36, 36, 115, 115, 36, 4, 11, 11, 7, 7, 7, 5, 5, 3, 3, 15, 15, 115, 115, 115, 115, 115, 36, 11, 11, 11, 11, 11, 11, 11] 201 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 361 number of broken/clashed sets: 116 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312606 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(CC1=NOC(C2CC2)=C1)C(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 8, 12, 1, 5, 5, 5, 1, 5, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [59, 59, 55, 36, 36, 36, 36, 51, 80, 80, 80, 80, 36, 36, 19, 9, 1, 1, 1, 1, 1, 1, 12, 12, 1, 19, 39, 39, 59, 59, 59, 55, 55, 51, 51, 9, 9, 12, 12, 12, 12, 12, 1, 39, 39, 39, 39, 39, 39, 39] 201 rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 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: 467 number of broken/clashed sets: 116 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312606 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(CC1=NOC(C2CC2)=C1)C(C)C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', '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', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 8, 12, 1, 5, 5, 5, 1, 5, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 18, 8, 8, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 17, 50, 85, 85, 85, 85, 170, 170, 85, 17, 33, 33, 20, 20, 20, 18, 18, 4, 4, 50, 50, 170, 170, 170, 170, 170, 85, 33, 33, 33, 33, 33, 33, 33] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 642 number of broken/clashed sets: 117 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312606 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312606 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312606/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312606/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312606 Building REAL300020312607 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312607' /scratch/stefan/7770667/working/building/REAL300020312607 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312607 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312607/0 /scratch/stefan/7770667/working/building/REAL300020312607 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/157 `/scratch/stefan/7770667/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2CCCCC21) `REAL300020312607.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312607 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2CCCCC21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 5, 9, 15, 15, 15, 15, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 5, 5, 5, 5, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 59 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 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: 101 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312607 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2CCCCC21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 13, 4, 4, 4, 4, 19, 27, 37, 37, 37, 37, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 13, 13, 19, 19, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 59 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 226 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312607 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2CCCCC21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 19, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 20, 20, 20, 19, 19, 6, 6, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 24 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312607 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312607/1 /scratch/stefan/7770667/working/building/REAL300020312607 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/158 `/scratch/stefan/7770667/working/3D/158' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2CCCCC21) `REAL300020312607.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312607 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2CCCCC21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 11, 5, 1, 1, 1, 1, 5, 9, 15, 15, 15, 15, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 5, 5, 5, 5, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 60 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 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: 101 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312607 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2CCCCC21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 23, 13, 4, 4, 4, 4, 19, 28, 38, 38, 38, 38, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 13, 13, 19, 19, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 60 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 232 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312607 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2CCCCC21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 19, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 20, 20, 20, 19, 19, 6, 6, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 24 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312607 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312607 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312607/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312607/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312607 Building REAL300020312608 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312608' /scratch/stefan/7770667/working/building/REAL300020312608 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312608 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312608/0 /scratch/stefan/7770667/working/building/REAL300020312608 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/159 `/scratch/stefan/7770667/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2CCCCC21) `REAL300020312608.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312608 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2CCCCC21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 11, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 39 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 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: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312608 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2CCCCC21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 18, 12, 5, 5, 5, 5, 14, 22, 22, 22, 22, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 12, 12, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 39 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 130 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312608 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2CCCCC21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [35, 35, 22, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 22, 22, 22, 22, 22, 22, 22, 22, 35, 35, 35, 22, 22, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 39 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 168 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312608 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312608/1 /scratch/stefan/7770667/working/building/REAL300020312608 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/160 `/scratch/stefan/7770667/working/3D/160' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2CCCCC21) `REAL300020312608.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312608/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312608 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2CCCCC21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 11, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 39 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 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: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312608 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2CCCCC21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [18, 18, 12, 5, 5, 5, 5, 14, 22, 22, 22, 22, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 12, 12, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 39 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 130 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312608 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2CCCCC21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [35, 35, 22, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 22, 22, 22, 22, 22, 22, 22, 22, 35, 35, 35, 22, 22, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 39 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 168 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312608 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312608 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312608/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312608/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312608 Building REAL300020312609 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312609' /scratch/stefan/7770667/working/building/REAL300020312609 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312609 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312609/0 /scratch/stefan/7770667/working/building/REAL300020312609 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/161 `/scratch/stefan/7770667/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CCC2CCCCC21) `REAL300020312609.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312609 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CCC2CCCCC21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 16, 5, 5, 5, 5, 13, 13, 5, 5, 16, 16, 16, 16, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 16, 16, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 26 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 1, 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]) total number of confs: 136 number of broken/clashed sets: 3 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312609 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CCC2CCCCC21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 7, 1, 1, 1, 1, 4, 4, 1, 1, 8, 8, 8, 8, 4, 4, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 7, 7, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 26 rigid atoms, others: [3, 4, 5, 6, 17, 18, 19, 20] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 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: 86 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312609 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CCC2CCCCC21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 19, 8, 8, 2, 2, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 23, 23, 23, 19, 19, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 26 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 110 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312609 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CCC2CCCCC21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 12, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 21, 12, 12, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 26 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 15, 16, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 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: 107 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312609 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312609/1 /scratch/stefan/7770667/working/building/REAL300020312609 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/162 `/scratch/stefan/7770667/working/3D/162' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CCC2CCCCC21) `REAL300020312609.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312609 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CCC2CCCCC21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 16, 5, 5, 5, 5, 13, 13, 6, 8, 16, 16, 16, 16, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 16, 16, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 26 rigid atoms, others: [19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 1, 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]) total number of confs: 137 number of broken/clashed sets: 3 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312609 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CCC2CCCCC21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 7, 1, 1, 1, 1, 4, 4, 1, 2, 8, 8, 8, 8, 4, 4, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 7, 7, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 26 rigid atoms, others: [3, 4, 5, 6, 17, 18, 19, 20] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 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: 88 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312609 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CCC2CCCCC21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 19, 8, 8, 1, 1, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 23, 23, 23, 19, 19, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16] 26 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 103 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312609 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CCC2CCCCC21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 12, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 21, 21, 21, 12, 12, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 26 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 15, 16, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 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: 107 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312609 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312609 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312609/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312609/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312609 Building REAL300020312610 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312610' /scratch/stefan/7770667/working/building/REAL300020312610 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312610 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312610/0 /scratch/stefan/7770667/working/building/REAL300020312610 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/163 `/scratch/stefan/7770667/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N(CC)CC(O)CC) `REAL300020312610.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312610 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N(CC)CC(O)CC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [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, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 5, 1, 1, 1, 1, 5, 7, 12, 12, 12, 12, 1, 1, 1, 1, 4, 10, 4, 14, 31, 30, 42, 9, 9, 9, 5, 5, 5, 5, 7, 7, 10, 10, 10, 10, 10, 14, 14, 31, 93, 42, 42, 42, 42, 42] 603 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 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: 387 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312610 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N(CC)CC(O)CC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [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, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 29, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 35, 82, 35, 91, 151, 147, 166, 31, 31, 31, 29, 29, 6, 6, 4, 4, 82, 82, 82, 82, 82, 91, 91, 151, 453, 166, 166, 166, 166, 166] 603 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 1515 number of broken/clashed sets: 75 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312610 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312610/1 /scratch/stefan/7770667/working/building/REAL300020312610 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/164 `/scratch/stefan/7770667/working/3D/164' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N(CC)CC(O)CC) `REAL300020312610.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312610 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N(CC)CC(O)CC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [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, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 5, 1, 1, 1, 1, 5, 7, 12, 12, 12, 12, 1, 1, 1, 1, 4, 10, 4, 14, 30, 29, 41, 9, 9, 9, 5, 5, 5, 5, 7, 7, 10, 10, 10, 10, 10, 14, 14, 30, 90, 41, 41, 41, 41, 41] 603 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 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: 378 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312610 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N(CC)CC(O)CC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [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, 7] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 29, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 34, 80, 34, 90, 151, 147, 165, 31, 31, 31, 29, 29, 6, 6, 4, 4, 80, 80, 80, 80, 80, 90, 90, 151, 453, 165, 165, 165, 165, 165] 603 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 1507 number of broken/clashed sets: 75 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312610 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312610 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312610/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312610/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312610 Building REAL300020312611 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312611' /scratch/stefan/7770667/working/building/REAL300020312611 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312611 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312611/0 /scratch/stefan/7770667/working/building/REAL300020312611 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/165 `/scratch/stefan/7770667/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(CC)CC(O)CC) `REAL300020312611.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312611 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(CC)CC(O)CC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [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] 1 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: [3, 3, 3, 1, 1, 1, 1, 2, 5, 5, 5, 5, 1, 1, 1, 1, 5, 8, 5, 9, 17, 17, 19, 3, 3, 3, 3, 3, 2, 2, 8, 8, 8, 8, 8, 9, 9, 17, 51, 19, 19, 19, 19, 19] 111 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 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: 166 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312611 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(CC)CC(O)CC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 276 conformations in input total number of sets (complete confs): 276 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 17, 9, 9, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 17, 30, 17, 31, 56, 54, 61, 24, 24, 24, 17, 17, 3, 3, 30, 30, 30, 30, 30, 31, 31, 56, 168, 61, 61, 61, 61, 61] 276 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 570 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312611 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312611/1 /scratch/stefan/7770667/working/building/REAL300020312611 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/166 `/scratch/stefan/7770667/working/3D/166' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(CC)CC(O)CC) `REAL300020312611.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312611 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(CC)CC(O)CC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [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] 1 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: [3, 3, 3, 1, 1, 1, 1, 2, 5, 5, 5, 5, 1, 1, 1, 1, 5, 8, 5, 9, 17, 17, 19, 3, 3, 3, 3, 3, 2, 2, 8, 8, 8, 8, 8, 9, 9, 17, 51, 19, 19, 19, 19, 19] 111 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 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: 166 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312611 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(CC)CC(O)CC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [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] 1 hydrogens need rotated 276 conformations in input total number of sets (complete confs): 276 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 17, 9, 9, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 17, 30, 17, 31, 56, 54, 61, 24, 24, 24, 17, 17, 3, 3, 30, 30, 30, 30, 30, 31, 31, 56, 168, 61, 61, 61, 61, 61] 276 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 570 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312611 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312611 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312611/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312611/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312611 Building REAL300020312612 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312612' /scratch/stefan/7770667/working/building/REAL300020312612 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312612 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312612/0 /scratch/stefan/7770667/working/building/REAL300020312612 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/167 `/scratch/stefan/7770667/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N(CC)CC(O)CC) `REAL300020312612.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312612 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N(CC)CC(O)CC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 279 conformations in input total number of sets (complete confs): 279 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 5, 1, 1, 1, 1, 4, 4, 3, 3, 8, 8, 8, 8, 4, 4, 1, 1, 1, 1, 4, 12, 4, 14, 38, 36, 54, 6, 6, 6, 5, 5, 4, 4, 4, 4, 12, 12, 12, 12, 12, 14, 14, 38, 114, 53, 53, 54, 54, 54] 279 rigid atoms, others: [3, 4, 5, 6, 17, 18, 19, 20] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 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: 427 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312612 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N(CC)CC(O)CC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 246 conformations in input total number of sets (complete confs): 246 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 8, 8, 2, 2, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 22, 42, 22, 52, 77, 76, 80, 16, 16, 16, 16, 16, 5, 5, 5, 5, 42, 42, 42, 42, 42, 52, 52, 77, 231, 80, 79, 80, 80, 80] 246 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 719 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312612 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N(CC)CC(O)CC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 279 conformations in input total number of sets (complete confs): 279 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 10, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 4, 4, 4, 4, 10, 27, 10, 34, 70, 68, 81, 11, 11, 11, 10, 10, 1, 1, 1, 1, 27, 27, 27, 27, 27, 34, 34, 70, 210, 80, 80, 81, 81, 81] 279 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 15, 16] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 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: 684 number of broken/clashed sets: 98 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312612 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312612/1 /scratch/stefan/7770667/working/building/REAL300020312612 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/168 `/scratch/stefan/7770667/working/3D/168' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N(CC)CC(O)CC) `REAL300020312612.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312612 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N(CC)CC(O)CC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 282 conformations in input total number of sets (complete confs): 282 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 5, 1, 1, 1, 1, 4, 4, 1, 1, 8, 8, 8, 8, 4, 4, 1, 1, 1, 1, 4, 13, 4, 14, 39, 37, 56, 6, 6, 6, 5, 5, 4, 4, 4, 4, 13, 13, 13, 13, 13, 14, 14, 39, 117, 55, 55, 56, 56, 56] 282 rigid atoms, others: [3, 4, 5, 6, 17, 18, 19, 20] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 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: 445 number of broken/clashed sets: 95 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312612 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N(CC)CC(O)CC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 246 conformations in input total number of sets (complete confs): 246 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 8, 8, 2, 2, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 22, 42, 22, 51, 76, 75, 80, 16, 16, 16, 16, 16, 4, 4, 4, 4, 42, 42, 42, 42, 42, 51, 51, 76, 228, 80, 79, 80, 80, 80] 246 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 711 number of broken/clashed sets: 73 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312612 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N(CC)CC(O)CC NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 282 conformations in input total number of sets (complete confs): 282 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 10, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 4, 4, 4, 4, 10, 28, 10, 33, 70, 68, 82, 11, 11, 11, 10, 10, 1, 1, 1, 1, 28, 28, 28, 28, 28, 33, 33, 70, 210, 81, 81, 82, 82, 82] 282 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 15, 16] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 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: 696 number of broken/clashed sets: 95 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312612 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312612 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312612/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312612/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312612 Building REAL300020312613 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312613' /scratch/stefan/7770667/working/building/REAL300020312613 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312613 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312613/0 /scratch/stefan/7770667/working/building/REAL300020312613 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/169 `/scratch/stefan/7770667/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N(CC)CCCCO) `REAL300020312613.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312613 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N(CC)CCCCO NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 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, 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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 5, 7, 12, 12, 12, 12, 1, 1, 1, 1, 4, 10, 4, 12, 17, 31, 62, 5, 5, 5, 5, 5, 5, 5, 7, 7, 10, 10, 10, 10, 10, 12, 12, 20, 20, 31, 31, 62, 62, 186] 603 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 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.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312613 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N(CC)CCCCO NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 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, 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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 24, 12, 12, 4, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 33, 63, 33, 81, 109, 156, 193, 24, 24, 24, 24, 24, 4, 4, 4, 4, 63, 63, 63, 63, 63, 81, 81, 124, 124, 155, 156, 193, 193, 579] 603 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 1799 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312613 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312613/1 /scratch/stefan/7770667/working/building/REAL300020312613 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/170 `/scratch/stefan/7770667/working/3D/170' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N(CC)CCCCO) `REAL300020312613.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312613 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N(CC)CCCCO NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 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, 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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 5, 7, 12, 12, 12, 12, 1, 1, 1, 1, 4, 10, 4, 12, 17, 31, 62, 5, 5, 5, 5, 5, 5, 5, 7, 7, 10, 10, 10, 10, 10, 12, 12, 20, 20, 31, 31, 62, 62, 186] 603 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 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.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312613 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N(CC)CCCCO NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 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, 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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 12, 12, 4, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 33, 63, 33, 81, 110, 157, 194, 23, 23, 23, 23, 23, 4, 4, 4, 4, 63, 63, 63, 63, 63, 81, 81, 125, 125, 156, 157, 194, 194, 582] 603 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 1802 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312613 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312613 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312613/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312613/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312613 Building REAL300020312614 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312614' /scratch/stefan/7770667/working/building/REAL300020312614 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312614 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312614/0 /scratch/stefan/7770667/working/building/REAL300020312614 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/171 `/scratch/stefan/7770667/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(CC)CCCCO) `REAL300020312614.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312614 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(CC)CCCCO NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 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, 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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 5, 1, 1, 1, 1, 2, 5, 5, 5, 5, 1, 1, 1, 1, 4, 12, 4, 14, 20, 43, 71, 8, 8, 8, 5, 5, 2, 2, 12, 12, 12, 12, 12, 14, 14, 24, 24, 40, 42, 71, 71, 213] 603 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 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: 654 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312614 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(CC)CCCCO NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 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, 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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 14, 6, 6, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 14, 32, 14, 44, 62, 101, 146, 20, 20, 20, 14, 14, 3, 3, 32, 32, 32, 32, 32, 44, 44, 72, 72, 96, 99, 146, 146, 438] 603 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 1338 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312614 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312614/1 /scratch/stefan/7770667/working/building/REAL300020312614 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/172 `/scratch/stefan/7770667/working/3D/172' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(CC)CCCCO) `REAL300020312614.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312614/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312614 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(CC)CCCCO NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 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, 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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 5, 1, 1, 1, 1, 2, 5, 5, 5, 5, 1, 1, 1, 1, 4, 12, 4, 14, 20, 44, 72, 8, 8, 8, 5, 5, 2, 2, 12, 12, 12, 12, 12, 14, 14, 25, 25, 41, 43, 72, 72, 216] 603 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 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: 668 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312614 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(CC)CCCCO NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 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, 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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 14, 6, 6, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 14, 32, 14, 44, 62, 101, 146, 20, 20, 20, 14, 14, 3, 3, 32, 32, 32, 32, 32, 44, 44, 72, 72, 96, 99, 146, 146, 438] 603 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 1338 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312614 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312614 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312614/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312614/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312614 Building REAL300020312615 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312615' /scratch/stefan/7770667/working/building/REAL300020312615 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312615 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312615/0 /scratch/stefan/7770667/working/building/REAL300020312615 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/173 `/scratch/stefan/7770667/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N(CC)CCCCO) `REAL300020312615.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312615 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N(CC)CCCCO NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 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, 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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 5, 1, 1, 1, 1, 4, 4, 1, 1, 9, 9, 9, 9, 4, 4, 1, 1, 1, 1, 4, 12, 4, 17, 24, 54, 111, 6, 6, 6, 5, 5, 4, 4, 4, 4, 12, 12, 12, 12, 12, 17, 17, 29, 29, 51, 53, 112, 112, 333] 603 rigid atoms, others: [3, 4, 5, 6, 17, 18, 19, 20] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 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: 966 number of broken/clashed sets: 141 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312615 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N(CC)CCCCO NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 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, 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] 1 hydrogens need rotated 585 conformations in input total number of sets (complete confs): 585 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 9, 9, 2, 1, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 9, 24, 62, 24, 85, 104, 164, 188, 22, 22, 22, 22, 22, 4, 4, 4, 4, 62, 62, 62, 62, 62, 85, 85, 118, 118, 159, 163, 188, 188, 564] 585 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 1732 number of broken/clashed sets: 138 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312615 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N(CC)CCCCO NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 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, 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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 12, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 4, 4, 4, 4, 10, 29, 10, 43, 59, 119, 177, 13, 13, 13, 12, 12, 1, 1, 1, 1, 29, 29, 29, 29, 29, 43, 43, 70, 70, 114, 117, 178, 178, 531] 603 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 15, 16] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 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: 1570 number of broken/clashed sets: 141 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312615 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312615/1 /scratch/stefan/7770667/working/building/REAL300020312615 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/174 `/scratch/stefan/7770667/working/3D/174' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N(CC)CCCCO) `REAL300020312615.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312615/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312615 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N(CC)CCCCO NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 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, 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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 5, 1, 1, 1, 1, 4, 4, 2, 4, 10, 10, 10, 10, 4, 4, 1, 1, 1, 1, 4, 12, 4, 17, 24, 54, 111, 6, 6, 6, 5, 5, 4, 4, 4, 4, 12, 12, 12, 12, 12, 17, 17, 29, 29, 51, 53, 112, 112, 333] 603 rigid atoms, others: [3, 4, 5, 6, 17, 18, 19, 20] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 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: 974 number of broken/clashed sets: 138 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312615 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N(CC)CCCCO NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 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, 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] 1 hydrogens need rotated 591 conformations in input total number of sets (complete confs): 591 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 23, 10, 10, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 10, 10, 10, 10, 25, 62, 25, 86, 105, 167, 190, 23, 23, 23, 23, 23, 3, 3, 3, 3, 62, 62, 62, 62, 62, 86, 86, 119, 119, 161, 166, 190, 190, 570] 591 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 1729 number of broken/clashed sets: 141 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312615 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N(CC)CCCCO NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 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, 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] 1 hydrogens need rotated 603 conformations in input total number of sets (complete confs): 603 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 12, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 4, 4, 4, 4, 10, 29, 10, 43, 60, 121, 178, 13, 13, 13, 12, 12, 1, 1, 1, 1, 29, 29, 29, 29, 29, 43, 43, 72, 72, 115, 119, 179, 179, 534] 603 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 15, 16] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 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: 1579 number of broken/clashed sets: 138 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312615 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312615 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312615/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312615/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312615 Building REAL300020312616 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312616' /scratch/stefan/7770667/working/building/REAL300020312616 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312616 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312616/0 /scratch/stefan/7770667/working/building/REAL300020312616 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/175 `/scratch/stefan/7770667/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1NC1=CC=CC(OC2CCC2)=C1) `REAL300020312616.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312616 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1NC1=CC=CC(OC2CCC2)=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [150, 150, 147, 89, 89, 89, 89, 188, 195, 197, 197, 197, 197, 89, 89, 72, 21, 21, 21, 21, 21, 7, 1, 1, 1, 1, 1, 21, 150, 150, 150, 147, 147, 188, 188, 195, 195, 72, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 21] 201 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 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, 48]) total number of confs: 1058 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312616 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1NC1=CC=CC(OC2CCC2)=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 4, 2, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 1, 1, 6, 16, 16, 16, 16, 16, 52, 89, 89, 89, 16, 4, 4, 4, 2, 2, 5, 5, 7, 7, 6, 16, 16, 16, 89, 89, 89, 89, 89, 89, 89, 16] 201 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 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: 263 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312616 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1NC1=CC=CC(OC2CCC2)=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [30, 30, 28, 16, 16, 16, 16, 53, 57, 67, 67, 67, 67, 16, 16, 9, 1, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 1, 30, 30, 30, 28, 28, 53, 53, 57, 57, 9, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 1] 201 rigid atoms, others: [48, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312616 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1NC1=CC=CC(OC2CCC2)=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [17, 17, 17, 12, 12, 6, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 27, 68, 68, 68, 68, 68, 141, 196, 196, 196, 68, 17, 17, 17, 17, 17, 6, 6, 4, 4, 27, 68, 68, 68, 196, 196, 196, 196, 196, 196, 196, 68] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 496 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312616 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312616/1 /scratch/stefan/7770667/working/building/REAL300020312616 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/176 `/scratch/stefan/7770667/working/3D/176' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1NC1=CC=CC(OC2CCC2)=C1) `REAL300020312616.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312616/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312616 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1NC1=CC=CC(OC2CCC2)=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [152, 152, 149, 91, 91, 91, 91, 190, 194, 196, 196, 196, 196, 91, 91, 74, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 1, 21, 152, 152, 152, 149, 149, 190, 190, 194, 194, 74, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 21] 201 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 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, 48]) total number of confs: 1039 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312616 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1NC1=CC=CC(OC2CCC2)=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 4, 2, 1, 1, 1, 1, 5, 7, 9, 9, 9, 9, 1, 1, 1, 1, 6, 16, 16, 16, 16, 16, 53, 91, 91, 91, 16, 4, 4, 4, 2, 2, 5, 5, 7, 7, 6, 16, 16, 16, 91, 91, 91, 91, 91, 91, 91, 16] 201 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 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: 266 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312616 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1NC1=CC=CC(OC2CCC2)=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [30, 30, 28, 16, 16, 16, 16, 53, 56, 66, 66, 66, 66, 16, 16, 9, 1, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 1, 30, 30, 30, 28, 28, 53, 53, 56, 56, 9, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 1] 201 rigid atoms, others: [48, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 347 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312616 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1NC1=CC=CC(OC2CCC2)=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [17, 17, 17, 11, 11, 6, 4, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 27, 70, 70, 70, 70, 70, 142, 195, 195, 195, 70, 17, 17, 17, 17, 17, 6, 6, 4, 4, 27, 70, 70, 70, 195, 195, 195, 195, 195, 195, 195, 70] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 498 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312616 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312616 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312616/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312616/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312616 Building REAL300020312617 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312617' /scratch/stefan/7770667/working/building/REAL300020312617 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312617 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312617/0 /scratch/stefan/7770667/working/building/REAL300020312617 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/177 `/scratch/stefan/7770667/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1NC1=CC=CC(OC2CCC2)=C1) `REAL300020312617.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312617 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1NC1=CC=CC(OC2CCC2)=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [186, 186, 177, 131, 131, 131, 131, 173, 179, 179, 179, 179, 131, 131, 86, 21, 21, 21, 21, 21, 7, 1, 1, 1, 1, 1, 21, 186, 186, 186, 177, 177, 173, 173, 86, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 21] 201 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 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, 45]) total number of confs: 859 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312617 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1NC1=CC=CC(OC2CCC2)=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [4, 4, 2, 1, 1, 1, 1, 3, 5, 5, 5, 5, 1, 1, 1, 1, 8, 32, 32, 32, 32, 32, 106, 131, 131, 131, 32, 4, 4, 4, 2, 2, 3, 3, 8, 32, 32, 32, 131, 131, 131, 131, 131, 131, 131, 32] 201 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 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: 272 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312617 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1NC1=CC=CC(OC2CCC2)=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [57, 57, 49, 32, 32, 32, 32, 49, 57, 57, 57, 57, 32, 31, 13, 1, 1, 1, 1, 1, 1, 1, 11, 21, 21, 21, 1, 57, 57, 57, 49, 49, 49, 49, 13, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 1] 201 rigid atoms, others: [35, 36, 37, 45, 15, 16, 17, 18, 19, 20, 21, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 369 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312617 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1NC1=CC=CC(OC2CCC2)=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 9, 5, 5, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 17, 58, 58, 58, 58, 58, 166, 182, 182, 182, 58, 11, 11, 11, 9, 9, 3, 3, 17, 58, 58, 58, 182, 182, 182, 182, 182, 182, 182, 58] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 343 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312617 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312617/1 /scratch/stefan/7770667/working/building/REAL300020312617 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/178 `/scratch/stefan/7770667/working/3D/178' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1NC1=CC=CC(OC2CCC2)=C1) `REAL300020312617.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312617/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312617 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1NC1=CC=CC(OC2CCC2)=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [186, 186, 177, 132, 132, 132, 132, 174, 175, 175, 175, 175, 132, 132, 87, 21, 21, 21, 21, 21, 7, 1, 1, 1, 1, 1, 21, 186, 186, 186, 177, 177, 174, 174, 87, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 21] 201 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 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, 45]) total number of confs: 845 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312617 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1NC1=CC=CC(OC2CCC2)=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [4, 4, 2, 1, 1, 1, 1, 3, 5, 5, 5, 5, 1, 1, 1, 1, 8, 32, 32, 32, 32, 32, 106, 132, 132, 132, 32, 4, 4, 4, 2, 2, 3, 3, 8, 32, 32, 32, 132, 132, 132, 132, 132, 132, 132, 32] 201 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312617 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1NC1=CC=CC(OC2CCC2)=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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: [57, 57, 49, 32, 32, 32, 32, 49, 57, 57, 57, 57, 32, 31, 13, 1, 1, 1, 1, 1, 1, 1, 11, 21, 21, 21, 1, 57, 57, 57, 49, 49, 49, 49, 13, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 1] 201 rigid atoms, others: [35, 36, 37, 45, 15, 16, 17, 18, 19, 20, 21, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 369 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312617 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1NC1=CC=CC(OC2CCC2)=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 1, 1, 1, 1, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 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, 9, 5, 5, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 17, 57, 57, 57, 57, 57, 165, 180, 180, 180, 57, 11, 11, 11, 9, 9, 3, 3, 17, 57, 57, 57, 180, 180, 180, 180, 180, 180, 180, 57] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 337 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312617 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312617 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312617/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312617/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312617 Building REAL300020312618 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312618' /scratch/stefan/7770667/working/building/REAL300020312618 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312618 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312618/0 /scratch/stefan/7770667/working/building/REAL300020312618 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/179 `/scratch/stefan/7770667/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC(=O)N(C)[C@@H]2C[C@@H]21) `REAL300020312618.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312618 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC(=O)N(C)[C@@H]2C[C@@H]21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 7, 7, 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, 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 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 5, 1, 1, 1, 1, 6, 10, 17, 17, 17, 17, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 5, 5, 6, 6, 10, 10, 5, 5, 5, 5, 5, 5, 5] 69 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 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: 104 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312618 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC(=O)N(C)[C@@H]2C[C@@H]21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 7, 7, 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, 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 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 13, 5, 5, 5, 5, 21, 34, 45, 45, 45, 45, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 13, 13, 21, 21, 34, 34, 1, 1, 2, 2, 2, 1, 1] 69 rigid atoms, others: [36, 37, 41, 42, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 268 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312618 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC(=O)N(C)[C@@H]2C[C@@H]21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 7, 7, 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, 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 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 23, 14, 14, 10, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 23, 23, 10, 10, 4, 4, 25, 25, 25, 25, 25, 25, 25] 31 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 126 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312618 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312618/1 /scratch/stefan/7770667/working/building/REAL300020312618 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/180 `/scratch/stefan/7770667/working/3D/180' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC(=O)N(C)[C@@H]2C[C@@H]21) `REAL300020312618.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312618/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312618 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC(=O)N(C)[C@@H]2C[C@@H]21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 7, 7, 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, 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 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 5, 1, 1, 1, 1, 6, 10, 17, 17, 17, 17, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 5, 5, 6, 6, 10, 10, 5, 5, 5, 5, 5, 5, 5] 69 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 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: 104 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312618 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC(=O)N(C)[C@@H]2C[C@@H]21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 7, 7, 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, 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 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 13, 5, 5, 5, 5, 21, 34, 45, 45, 45, 45, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 13, 13, 21, 21, 34, 34, 1, 1, 2, 2, 2, 1, 1] 69 rigid atoms, others: [36, 37, 41, 42, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 268 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312618 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC(=O)N(C)[C@@H]2C[C@@H]21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 7, 7, 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, 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 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 22, 14, 14, 10, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 24, 24, 24, 22, 22, 10, 10, 4, 4, 25, 25, 25, 25, 25, 25, 25] 31 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 119 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312618 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312618 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312618/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312618/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312618 Building REAL300020312619 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312619' /scratch/stefan/7770667/working/building/REAL300020312619 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312619 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312619/0 /scratch/stefan/7770667/working/building/REAL300020312619 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/181 `/scratch/stefan/7770667/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC(=O)N(C)[C@@H]2C[C@@H]21) `REAL300020312619.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312619 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC(=O)N(C)[C@@H]2C[C@@H]21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 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, 7, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4] 41 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 60 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312619 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC(=O)N(C)[C@@H]2C[C@@H]21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 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, 7, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 9, 4, 4, 4, 4, 12, 18, 18, 18, 18, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 9, 9, 12, 12, 1, 1, 2, 2, 2, 1, 1] 41 rigid atoms, others: [33, 34, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 113 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312619 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC(=O)N(C)[C@@H]2C[C@@H]21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 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, 7, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 21, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 30, 30, 30, 21, 21, 3, 3, 18, 18, 18, 18, 18, 18, 18] 41 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 140 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312619 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312619/1 /scratch/stefan/7770667/working/building/REAL300020312619 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/182 `/scratch/stefan/7770667/working/3D/182' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC(=O)N(C)[C@@H]2C[C@@H]21) `REAL300020312619.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312619 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC(=O)N(C)[C@@H]2C[C@@H]21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 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, 7, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4] 41 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 60 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312619 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC(=O)N(C)[C@@H]2C[C@@H]21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 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, 7, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 9, 4, 4, 4, 4, 12, 18, 18, 18, 18, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 9, 9, 12, 12, 1, 1, 2, 2, 2, 1, 1] 41 rigid atoms, others: [33, 34, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 113 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312619 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC(=O)N(C)[C@@H]2C[C@@H]21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 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, 7, 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 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 21, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 30, 30, 30, 21, 21, 3, 3, 18, 18, 18, 18, 18, 18, 18] 41 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 140 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312619 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312619 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312619/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312619/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312619 Building REAL300020312620 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312620' /scratch/stefan/7770667/working/building/REAL300020312620 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312620 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312620/0 /scratch/stefan/7770667/working/building/REAL300020312620 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/183 `/scratch/stefan/7770667/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CC(=O)N(C)[C@@H]2C[C@@H]21) `REAL300020312620.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312620 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CC(=O)N(C)[C@@H]2C[C@@H]21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 7, 7, 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, 7, 7, 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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 14, 5, 5, 5, 5, 12, 12, 5, 5, 15, 15, 15, 15, 12, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 14, 14, 12, 12, 12, 12, 1, 1, 2, 2, 2, 1, 1] 22 rigid atoms, others: [40, 41, 45, 46, 19, 20, 21, 22, 23, 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, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 124 number of broken/clashed sets: 5 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312620 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CC(=O)N(C)[C@@H]2C[C@@H]21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 7, 7, 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, 7, 7, 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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 7, 1, 1, 1, 1, 4, 4, 1, 1, 8, 8, 8, 8, 4, 4, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 7, 7, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5] 22 rigid atoms, others: [3, 4, 5, 6, 17, 18, 19, 20] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 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: 71 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312620 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CC(=O)N(C)[C@@H]2C[C@@H]21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 7, 7, 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, 7, 7, 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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 17, 8, 8, 2, 2, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 20, 20, 20, 17, 17, 4, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15] 22 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 85 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312620 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CC(=O)N(C)[C@@H]2C[C@@H]21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 7, 7, 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, 7, 7, 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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 13, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 19, 13, 13, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12] 22 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 39, 15, 16, 38, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 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]) total number of confs: 91 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312620 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312620/1 /scratch/stefan/7770667/working/building/REAL300020312620 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/184 `/scratch/stefan/7770667/working/3D/184' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CC(=O)N(C)[C@@H]2C[C@@H]21) `REAL300020312620.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312620 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CC(=O)N(C)[C@@H]2C[C@@H]21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 7, 7, 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, 7, 7, 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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 14, 5, 5, 5, 5, 12, 12, 9, 9, 15, 15, 15, 15, 12, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 14, 14, 12, 12, 12, 12, 1, 1, 2, 2, 2, 1, 1] 22 rigid atoms, others: [40, 41, 45, 46, 19, 20, 21, 22, 23, 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, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44]) total number of confs: 114 number of broken/clashed sets: 5 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312620 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CC(=O)N(C)[C@@H]2C[C@@H]21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 7, 7, 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, 7, 7, 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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 7, 1, 1, 1, 1, 4, 4, 2, 2, 8, 8, 8, 8, 4, 4, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 7, 7, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5] 22 rigid atoms, others: [3, 4, 5, 6, 17, 18, 19, 20] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 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: 72 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312620 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CC(=O)N(C)[C@@H]2C[C@@H]21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 7, 7, 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, 7, 7, 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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 17, 8, 8, 1, 1, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 20, 20, 20, 17, 17, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15] 22 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 94 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312620 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CC(=O)N(C)[C@@H]2C[C@@H]21 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 7, 7, 7, 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, 7, 7, 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 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 13, 4, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 19, 19, 19, 13, 13, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12] 22 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 39, 15, 16, 38, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 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]) total number of confs: 91 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312620 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312620 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312620/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312620/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312620 Building REAL300020312621 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312621' /scratch/stefan/7770667/working/building/REAL300020312621 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312621 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312621/0 /scratch/stefan/7770667/working/building/REAL300020312621 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/185 `/scratch/stefan/7770667/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(CC(C)=NO2)CC1) `REAL300020312621.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312621 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(CC(C)=NO2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'N.2', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 5, 8, 12, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 6, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 6, 6, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 63 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 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: 107 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312621 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(CC(C)=NO2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'N.2', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 5, 8, 12, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 13, 5, 5, 5, 5, 18, 27, 35, 35, 35, 35, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 13, 13, 18, 18, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 63 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 226 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312621 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(CC(C)=NO2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'N.2', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 5, 8, 12, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 18, 12, 12, 8, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 20, 20, 20, 18, 18, 8, 8, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 21 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 100 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312621 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312621/1 /scratch/stefan/7770667/working/building/REAL300020312621 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/186 `/scratch/stefan/7770667/working/3D/186' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(CC(C)=NO2)CC1) `REAL300020312621.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312621 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(CC(C)=NO2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'N.2', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 5, 8, 12, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 6, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 6, 6, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 63 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 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: 107 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312621 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(CC(C)=NO2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'N.2', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 5, 8, 12, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 13, 5, 5, 5, 5, 18, 27, 35, 35, 35, 35, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 13, 13, 18, 18, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 63 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 226 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312621 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(CC(C)=NO2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'N.2', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 5, 8, 12, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 18, 12, 12, 8, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 20, 20, 20, 18, 18, 8, 8, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 21 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 100 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312621 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312621 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312621/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312621/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312621 Building REAL300020312622 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312622' /scratch/stefan/7770667/working/building/REAL300020312622 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312622 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312622/0 /scratch/stefan/7770667/working/building/REAL300020312622 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/187 `/scratch/stefan/7770667/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(CC(C)=NO2)CC1) `REAL300020312622.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312622 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(CC(C)=NO2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'N.2', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 5, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 6, 1, 1, 1, 1, 7, 9, 9, 9, 9, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 6, 6, 7, 7, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 39 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 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: 79 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312622 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(CC(C)=NO2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'N.2', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 5, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 13, 5, 5, 5, 5, 15, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 13, 13, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 39 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 123 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312622 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(CC(C)=NO2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'N.2', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 5, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 24, 9, 9, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 35, 35, 35, 24, 24, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 39 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 161 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312622 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312622/1 /scratch/stefan/7770667/working/building/REAL300020312622 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/188 `/scratch/stefan/7770667/working/3D/188' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(CC(C)=NO2)CC1) `REAL300020312622.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312622 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(CC(C)=NO2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'N.2', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 5, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 6, 1, 1, 1, 1, 7, 9, 9, 9, 9, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 6, 6, 7, 7, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 39 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 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: 79 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312622 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(CC(C)=NO2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'N.2', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 5, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 13, 5, 5, 5, 5, 15, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 13, 13, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 39 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 123 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312622 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(CC(C)=NO2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'N.2', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 5, 8, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 24, 9, 9, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 35, 35, 35, 24, 24, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 39 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 161 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312622 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312622 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312622/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312622/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312622 Building REAL300020312623 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312623' /scratch/stefan/7770667/working/building/REAL300020312623 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312623 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312623/0 /scratch/stefan/7770667/working/building/REAL300020312623 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/189 `/scratch/stefan/7770667/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(CC#N)C(F)(F)CC1) `REAL300020312623.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) Killed Solvation calculation failed Skipping REAL300020312623 0 /scratch/stefan/7770667/working/building/REAL300020312623 /scratch/stefan/7770667/working /scratch/stefan/7770667 `0' -> `0.failed' Finished preparing REAL300020312623 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Found failed protomers Marking REAL300020312623 as failed mkdir: created directory `/scratch/stefan/7770667/failed' `/scratch/stefan/7770667/working/building/REAL300020312623' -> `/scratch/stefan/7770667/failed/REAL300020312623' Building REAL300020312624 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312624' /scratch/stefan/7770667/working/building/REAL300020312624 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312624 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312624/0 /scratch/stefan/7770667/working/building/REAL300020312624 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/191 `/scratch/stefan/7770667/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(CC#N)C(F)(F)CC1) `REAL300020312624.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312624 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(CC#N)C(F)(F)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 8, 5, 15, 15, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 9, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 6, 6, 6, 6, 17, 17, 6, 6, 6, 6, 6, 9, 9, 9, 5, 5, 6, 6, 6, 6, 6, 6, 6, 17, 17, 6, 6, 6, 6] 98 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 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: 110 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312624 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(CC#N)C(F)(F)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 8, 5, 15, 15, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 13, 6, 6, 6, 6, 16, 22, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 1, 1, 1, 20, 20, 20, 13, 13, 16, 16, 1, 1, 1, 1, 1, 7, 7, 1, 1, 1, 1] 98 rigid atoms, others: [34, 35, 36, 37, 38, 41, 42, 43, 44, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 27, 28, 29, 30, 31, 32, 33, 39, 40]) total number of confs: 151 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312624 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(CC#N)C(F)(F)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 8, 5, 15, 15, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 23, 8, 8, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 22, 22, 22, 22, 57, 57, 22, 22, 22, 22, 22, 31, 31, 31, 23, 23, 3, 3, 22, 22, 22, 22, 22, 57, 57, 22, 22, 22, 22] 98 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 300 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312624 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312624/1 /scratch/stefan/7770667/working/building/REAL300020312624 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/192 `/scratch/stefan/7770667/working/3D/192' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(CC#N)C(F)(F)CC1) `REAL300020312624.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312624 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(CC#N)C(F)(F)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 8, 5, 15, 15, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 9, 5, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 6, 6, 6, 6, 17, 17, 6, 6, 6, 6, 6, 9, 9, 9, 5, 5, 6, 6, 6, 6, 6, 6, 6, 17, 17, 6, 6, 6, 6] 98 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 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: 110 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312624 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(CC#N)C(F)(F)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 8, 5, 15, 15, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 20, 13, 6, 6, 6, 6, 16, 22, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 1, 7, 7, 1, 1, 1, 1, 1, 20, 20, 20, 13, 13, 16, 16, 1, 1, 1, 1, 1, 7, 7, 1, 1, 1, 1] 98 rigid atoms, others: [34, 35, 36, 37, 38, 41, 42, 43, 44, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 27, 28, 29, 30, 31, 32, 33, 39, 40]) total number of confs: 151 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312624 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(CC#N)C(F)(F)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.1', 'N.1', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 8, 5, 15, 15, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [31, 31, 23, 8, 8, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 22, 22, 22, 22, 57, 57, 22, 22, 22, 22, 22, 31, 31, 31, 23, 23, 3, 3, 22, 22, 22, 22, 22, 57, 57, 22, 22, 22, 22] 98 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 300 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312624 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312624 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312624/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312624/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312624 Building REAL300020312625 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312625' /scratch/stefan/7770667/working/building/REAL300020312625 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312625 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312625/0 /scratch/stefan/7770667/working/building/REAL300020312625 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/193 `/scratch/stefan/7770667/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(CC1)CC(=O)NCC2O) `REAL300020312625.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312625 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(CC1)CC(=O)NCC2O NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 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, 4, 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 hydrogens 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, 6, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 6, 6, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15] 201 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 122 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312625 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(CC1)CC(=O)NCC2O NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 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, 4, 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 hydrogens 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, 13, 5, 5, 5, 5, 18, 29, 36, 36, 36, 36, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 13, 13, 18, 18, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6] 201 rigid atoms, others: [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, 50, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31, 32, 33, 34, 35, 36, 37, 52]) total number of confs: 242 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312625 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(CC1)CC(=O)NCC2O NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 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, 4, 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 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: [22, 22, 20, 13, 13, 8, 4, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 22, 22, 22, 20, 20, 8, 8, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 54] 69 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 152 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312625 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312625/1 /scratch/stefan/7770667/working/building/REAL300020312625 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/194 `/scratch/stefan/7770667/working/3D/194' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(CC1)CC(=O)NCC2O) `REAL300020312625.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312625 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(CC1)CC(=O)NCC2O NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 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, 4, 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 hydrogens 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, 6, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 6, 6, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15] 201 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 122 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312625 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(CC1)CC(=O)NCC2O NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 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, 4, 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 hydrogens 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, 13, 5, 5, 5, 5, 18, 29, 36, 36, 36, 36, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 13, 13, 18, 18, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6] 201 rigid atoms, others: [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, 50, 51] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31, 32, 33, 34, 35, 36, 37, 52]) total number of confs: 242 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312625 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(CC1)CC(=O)NCC2O NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 7, 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, 4, 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 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: [22, 22, 20, 13, 13, 8, 4, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 22, 22, 22, 20, 20, 8, 8, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 54] 69 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 152 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312625 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312625 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312625/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312625/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312625 Building REAL300020312626 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312626' /scratch/stefan/7770667/working/building/REAL300020312626 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312626 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312626/0 /scratch/stefan/7770667/working/building/REAL300020312626 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/195 `/scratch/stefan/7770667/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(CC1)CC(=O)NCC2O) `REAL300020312626.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312626 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(CC1)CC(=O)NCC2O NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 7, 9, 9, 9, 9, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 5, 5, 7, 7, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15] 126 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 91 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312626 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(CC1)CC(=O)NCC2O NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 12, 5, 5, 5, 5, 16, 22, 22, 22, 22, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 12, 12, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6] 126 rigid atoms, others: [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, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30, 31, 32, 33, 34, 49]) total number of confs: 147 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312626 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(CC1)CC(=O)NCC2O NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 23, 9, 9, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 35, 35, 35, 23, 23, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 66] 126 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 232 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312626 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312626/1 /scratch/stefan/7770667/working/building/REAL300020312626 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/196 `/scratch/stefan/7770667/working/3D/196' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(CC1)CC(=O)NCC2O) `REAL300020312626.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312626 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(CC1)CC(=O)NCC2O NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 7, 9, 9, 9, 9, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 5, 5, 7, 7, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15] 126 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 91 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312626 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(CC1)CC(=O)NCC2O NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 12, 5, 5, 5, 5, 16, 22, 22, 22, 22, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 12, 12, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6] 126 rigid atoms, others: [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, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30, 31, 32, 33, 34, 49]) total number of confs: 147 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312626 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(CC1)CC(=O)NCC2O NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6] dock color type numbers: [7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 23, 9, 9, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 35, 35, 35, 23, 23, 3, 3, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 66] 126 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 232 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312626 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312626 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312626/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312626/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312626 Building REAL300020312627 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312627' /scratch/stefan/7770667/working/building/REAL300020312627 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312627 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312627/0 /scratch/stefan/7770667/working/building/REAL300020312627 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/197 `/scratch/stefan/7770667/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(CCC(=O)OC)C1) `REAL300020312627.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312627 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(CCC(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 3, 3, 1, 1, 1, 1, 5, 7, 12, 12, 12, 12, 1, 1, 1, 1, 5, 5, 5, 5, 14, 25, 96, 96, 96, 5, 3, 3, 3, 3, 3, 5, 5, 7, 7, 5, 5, 5, 5, 5, 14, 14, 25, 25, 96, 96, 96, 5, 5] 201 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312627 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(CCC(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 8, 8, 5, 5, 5, 5, 17, 19, 29, 29, 29, 29, 5, 5, 1, 1, 1, 1, 1, 1, 5, 9, 41, 41, 41, 1, 8, 8, 8, 8, 8, 17, 17, 19, 19, 1, 1, 1, 1, 1, 5, 5, 9, 9, 41, 41, 41, 1, 1] 201 rigid atoms, others: [48, 49, 36, 37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312627 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(CCC(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 21, 21, 15, 15, 6, 4, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 30, 30, 30, 30, 69, 97, 189, 189, 189, 30, 21, 21, 21, 21, 21, 6, 6, 4, 4, 30, 30, 30, 30, 30, 69, 69, 97, 97, 189, 189, 189, 30, 30] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 736 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312627 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312627/1 /scratch/stefan/7770667/working/building/REAL300020312627 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/198 `/scratch/stefan/7770667/working/3D/198' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(CCC(=O)OC)C1) `REAL300020312627.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312627/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312627 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(CCC(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 3, 3, 1, 1, 1, 1, 5, 7, 12, 12, 12, 12, 1, 1, 1, 1, 5, 5, 5, 5, 14, 25, 96, 96, 96, 5, 3, 3, 3, 3, 3, 5, 5, 7, 7, 5, 5, 5, 5, 5, 14, 14, 25, 25, 96, 96, 96, 5, 5] 201 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312627 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(CCC(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 8, 8, 5, 5, 5, 5, 17, 19, 29, 29, 29, 29, 5, 5, 1, 1, 1, 1, 1, 1, 5, 9, 41, 41, 41, 1, 8, 8, 8, 8, 8, 17, 17, 19, 19, 1, 1, 1, 1, 1, 5, 5, 9, 9, 41, 41, 41, 1, 1] 201 rigid atoms, others: [48, 49, 36, 37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312627 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(CCC(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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: [20, 20, 20, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 29, 29, 29, 29, 66, 91, 190, 190, 190, 29, 20, 20, 20, 20, 20, 6, 6, 4, 4, 29, 29, 29, 29, 29, 66, 66, 91, 91, 190, 190, 190, 29, 29] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 734 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312627 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312627 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312627/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312627/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312627 Building REAL300020312628 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312628' /scratch/stefan/7770667/working/building/REAL300020312628 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312628 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312628/0 /scratch/stefan/7770667/working/building/REAL300020312628 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/199 `/scratch/stefan/7770667/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(CCC(=O)OC)C1) `REAL300020312628.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312628 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(CCC(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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: [5, 5, 4, 1, 1, 1, 1, 2, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 5, 15, 24, 102, 102, 102, 5, 5, 5, 5, 4, 4, 2, 2, 5, 5, 5, 5, 5, 15, 15, 24, 24, 102, 102, 102, 5, 5] 201 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312628 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(CCC(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 10, 9, 5, 5, 5, 5, 8, 14, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 5, 8, 38, 38, 38, 1, 10, 10, 10, 9, 9, 8, 8, 1, 1, 1, 1, 1, 5, 5, 8, 8, 38, 38, 38, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 45, 14, 15, 16, 17, 18, 19, 46, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312628 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(CCC(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 11, 10, 4, 4, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 14, 14, 14, 14, 38, 55, 176, 176, 176, 14, 11, 11, 11, 10, 10, 3, 3, 14, 14, 14, 14, 14, 38, 38, 55, 55, 176, 176, 176, 14, 14] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 600 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312628 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312628/1 /scratch/stefan/7770667/working/building/REAL300020312628 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/200 `/scratch/stefan/7770667/working/3D/200' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(CCC(=O)OC)C1) `REAL300020312628.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312628 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(CCC(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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: [5, 5, 4, 1, 1, 1, 1, 2, 4, 4, 4, 4, 1, 1, 1, 1, 5, 5, 5, 5, 15, 24, 102, 102, 102, 5, 5, 5, 5, 4, 4, 2, 2, 5, 5, 5, 5, 5, 15, 15, 24, 24, 102, 102, 102, 5, 5] 201 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312628 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(CCC(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 10, 9, 5, 5, 5, 5, 8, 14, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 5, 8, 38, 38, 38, 1, 10, 10, 10, 9, 9, 8, 8, 1, 1, 1, 1, 1, 5, 5, 8, 8, 38, 38, 38, 1, 1] 201 rigid atoms, others: [33, 34, 35, 36, 37, 45, 14, 15, 16, 17, 18, 19, 46, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312628 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(CCC(=O)OC)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 5, 1, 11, 12, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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, 11, 10, 4, 4, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 14, 14, 14, 14, 38, 55, 176, 176, 176, 14, 11, 11, 11, 10, 10, 3, 3, 14, 14, 14, 14, 14, 38, 38, 55, 55, 176, 176, 176, 14, 14] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 600 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312628 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312628 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312628/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312628/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312628 Building REAL300020312629 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312629' /scratch/stefan/7770667/working/building/REAL300020312629 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312629 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312629/0 /scratch/stefan/7770667/working/building/REAL300020312629 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/201 `/scratch/stefan/7770667/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(C)CCCN(CC)C1=CC=CC=C1) `REAL300020312629.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312629 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(C)CCCN(CC)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 11, 17, 34, 111, 163, 111, 152, 152, 132, 152, 152, 3, 3, 3, 3, 3, 2, 2, 4, 4, 4, 11, 11, 19, 19, 33, 34, 170, 170, 163, 170, 170, 152, 139, 134, 152, 152] 201 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 877 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312629 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(C)CCCN(CC)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 174, 174, 152, 152, 152, 152, 175, 184, 184, 184, 184, 152, 152, 80, 42, 80, 20, 15, 6, 1, 6, 15, 1, 1, 1, 1, 1, 1, 174, 174, 174, 174, 174, 175, 175, 80, 80, 80, 42, 41, 22, 22, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1] 201 rigid atoms, others: [50, 51, 20, 53, 54, 23, 24, 25, 26, 27, 28, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 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: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312629 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N(C)CCCN(CC)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 4, 4, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 11, 21, 28, 42, 134, 189, 134, 181, 181, 161, 181, 181, 10, 10, 10, 9, 9, 3, 3, 11, 11, 11, 21, 21, 30, 30, 41, 42, 198, 198, 189, 198, 198, 181, 170, 163, 181, 181] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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, 54]) total number of confs: 1016 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312629 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312629/1 /scratch/stefan/7770667/working/building/REAL300020312629 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/202 `/scratch/stefan/7770667/working/3D/202' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(C)CCCN(CC)C1=CC=CC=C1) `REAL300020312629.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312629 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(C)CCCN(CC)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 11, 17, 34, 111, 163, 111, 153, 153, 133, 153, 153, 3, 3, 3, 3, 3, 2, 2, 4, 4, 4, 11, 11, 19, 19, 33, 34, 170, 170, 163, 170, 170, 153, 140, 147, 153, 153] 201 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 906 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312629 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(C)CCCN(CC)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 175, 153, 153, 153, 153, 176, 187, 187, 187, 187, 153, 153, 81, 42, 81, 20, 15, 6, 1, 6, 15, 1, 1, 1, 1, 1, 1, 175, 175, 175, 175, 175, 176, 176, 81, 81, 81, 42, 41, 22, 22, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1] 201 rigid atoms, others: [50, 51, 20, 53, 54, 23, 24, 25, 26, 27, 28, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 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: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312629 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N(C)CCCN(CC)C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 5, 5, 1, 1, 1, 1, 1, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 4, 4, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 11, 11, 21, 28, 42, 136, 191, 136, 183, 183, 163, 183, 183, 9, 9, 9, 8, 8, 3, 3, 11, 11, 11, 21, 21, 30, 30, 41, 42, 200, 200, 191, 200, 200, 183, 172, 178, 183, 183] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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, 54]) total number of confs: 1042 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312629 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312629 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312629/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312629/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312629 Building REAL300020312630 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312630' /scratch/stefan/7770667/working/building/REAL300020312630 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312630 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312630/0 /scratch/stefan/7770667/working/building/REAL300020312630 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/203 `/scratch/stefan/7770667/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2=CC=C(F)C=C2C1C) `REAL300020312630.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312630 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2=CC=C(F)C=C2C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 5, 1, 1, 1, 1, 5, 9, 13, 13, 13, 13, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 5, 5, 5, 5, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 36 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 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: 90 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312630 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2=CC=C(F)C=C2C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 8, 3, 3, 3, 3, 11, 18, 22, 22, 22, 22, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 8, 8, 11, 11, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 36 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47]) total number of confs: 141 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312630 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2=CC=C(F)C=C2C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 17, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 19, 19, 19, 17, 17, 5, 5, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 19 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 88 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312630 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312630/1 /scratch/stefan/7770667/working/building/REAL300020312630 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/204 `/scratch/stefan/7770667/working/3D/204' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2=CC=C(F)C=C2C1C) `REAL300020312630.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312630 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2=CC=C(F)C=C2C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 5, 1, 1, 1, 1, 5, 9, 13, 13, 13, 13, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 5, 5, 5, 5, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 36 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 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: 90 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312630 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2=CC=C(F)C=C2C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 8, 3, 3, 3, 3, 11, 18, 22, 22, 22, 22, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 8, 8, 11, 11, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 36 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47]) total number of confs: 141 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312630 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2=CC=C(F)C=C2C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 17, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 19, 19, 19, 17, 17, 5, 5, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 19 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 88 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312630 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312630 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312630/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312630/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312630 Building REAL300020312631 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312631' /scratch/stefan/7770667/working/building/REAL300020312631 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312631 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312631/0 /scratch/stefan/7770667/working/building/REAL300020312631 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/205 `/scratch/stefan/7770667/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2=CC=C(F)C=C2C1C) `REAL300020312631.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312631 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2=CC=C(F)C=C2C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 25 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 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: 62 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312631 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2=CC=C(F)C=C2C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 3, 3, 3, 3, 10, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 8, 8, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 25 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44]) total number of confs: 90 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312631 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2=CC=C(F)C=C2C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 25, 25, 25, 21, 21, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 25 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 112 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312631 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312631/1 /scratch/stefan/7770667/working/building/REAL300020312631 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/206 `/scratch/stefan/7770667/working/3D/206' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2=CC=C(F)C=C2C1C) `REAL300020312631.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312631/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312631 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2=CC=C(F)C=C2C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 9, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 25 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 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: 62 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312631 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2=CC=C(F)C=C2C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 8, 3, 3, 3, 3, 10, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 8, 8, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2] 25 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44]) total number of confs: 90 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312631 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2=CC=C(F)C=C2C1C NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 1, 1, 1, 1, 15, 1, 1, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 21, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 25, 25, 25, 21, 21, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 25 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 112 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312631 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312631 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312631/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312631/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312631 Building REAL300020312632 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312632' /scratch/stefan/7770667/working/building/REAL300020312632 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312632 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312632/0 /scratch/stefan/7770667/working/building/REAL300020312632 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/207 `/scratch/stefan/7770667/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC2=C(C1)C(=O)NC(=O)N2) `REAL300020312632.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312632 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC2=C(C1)C(=O)NC(=O)N2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 1, 11, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [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, 6, 4, 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: [11, 11, 5, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 5, 5, 5, 5, 9, 9, 6, 6, 6, 6, 6, 6] 90 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 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: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312632 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC2=C(C1)C(=O)NC(=O)N2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 1, 11, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [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, 6, 4, 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: [34, 34, 17, 6, 6, 6, 6, 25, 39, 52, 52, 52, 52, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 17, 17, 25, 25, 39, 39, 1, 1, 1, 1, 1, 1] 90 rigid atoms, others: [36, 37, 38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312632 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC2=C(C1)C(=O)NC(=O)N2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 1, 11, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [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, 6, 4, 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: [31, 31, 27, 14, 14, 8, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 27, 27, 8, 8, 4, 4, 31, 31, 31, 31, 31, 31] 41 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312632 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312632/1 /scratch/stefan/7770667/working/building/REAL300020312632 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/208 `/scratch/stefan/7770667/working/3D/208' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC2=C(C1)C(=O)NC(=O)N2) `REAL300020312632.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312632/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312632 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC2=C(C1)C(=O)NC(=O)N2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 1, 11, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [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, 6, 4, 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: [11, 11, 5, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 5, 5, 5, 5, 9, 9, 6, 6, 6, 6, 6, 6] 90 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 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: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312632 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC2=C(C1)C(=O)NC(=O)N2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 1, 11, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [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, 6, 4, 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: [34, 34, 17, 6, 6, 6, 6, 25, 39, 52, 52, 52, 52, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 17, 17, 25, 25, 39, 39, 1, 1, 1, 1, 1, 1] 90 rigid atoms, others: [36, 37, 38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312632 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC2=C(C1)C(=O)NC(=O)N2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 1, 11, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [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, 6, 4, 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: [31, 31, 27, 14, 14, 8, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 27, 27, 8, 8, 4, 4, 31, 31, 31, 31, 31, 31] 41 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 159 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312632 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312632 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312632/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312632/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312632 Building REAL300020312633 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312633' /scratch/stefan/7770667/working/building/REAL300020312633 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312633 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312633/0 /scratch/stefan/7770667/working/building/REAL300020312633 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/209 `/scratch/stefan/7770667/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC2=C(C1)C(=O)NC(=O)N2) `REAL300020312633.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312633 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC2=C(C1)C(=O)NC(=O)N2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 1, 11, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 7, 9, 9, 9, 9, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 5, 5, 7, 7, 6, 6, 6, 6, 6, 6] 59 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 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: 77 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312633 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC2=C(C1)C(=O)NC(=O)N2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 1, 11, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 16, 6, 6, 6, 6, 20, 27, 27, 27, 27, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 16, 16, 20, 20, 1, 1, 1, 1, 1, 1] 59 rigid atoms, others: [33, 34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 195 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312633 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC2=C(C1)C(=O)NC(=O)N2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 1, 11, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 21, 9, 9, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 30, 30, 30, 21, 21, 3, 3, 27, 27, 27, 27, 27, 27] 59 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 144 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312633 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312633/1 /scratch/stefan/7770667/working/building/REAL300020312633 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/210 `/scratch/stefan/7770667/working/3D/210' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC2=C(C1)C(=O)NC(=O)N2) `REAL300020312633.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312633 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC2=C(C1)C(=O)NC(=O)N2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 1, 11, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 7, 9, 9, 9, 9, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 5, 5, 7, 7, 6, 6, 6, 6, 6, 6] 59 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 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: 77 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312633 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC2=C(C1)C(=O)NC(=O)N2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 1, 11, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 16, 6, 6, 6, 6, 20, 27, 27, 27, 27, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 16, 16, 20, 20, 1, 1, 1, 1, 1, 1] 59 rigid atoms, others: [33, 34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 195 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312633 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC2=C(C1)C(=O)NC(=O)N2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 1, 5, 1, 11, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 21, 9, 9, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 30, 30, 30, 21, 21, 3, 3, 27, 27, 27, 27, 27, 27] 59 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 144 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312633 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312633 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312633/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312633/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312633 Building REAL300020312634 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312634' /scratch/stefan/7770667/working/building/REAL300020312634 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312634 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312634/0 /scratch/stefan/7770667/working/building/REAL300020312634 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/211 `/scratch/stefan/7770667/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC(=O)N2CCOCC2C1) `REAL300020312634.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312634 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC(=O)N2CCOCC2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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: [12, 12, 6, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 6, 6, 5, 5, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 65 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 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: 108 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312634 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC(=O)N2CCOCC2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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: [25, 25, 14, 6, 6, 6, 6, 18, 27, 38, 38, 38, 38, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 14, 14, 18, 18, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 65 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 221 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312634 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC(=O)N2CCOCC2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 23, 13, 13, 8, 4, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 27, 27, 27, 23, 23, 8, 8, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 29 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 132 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312634 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312634/1 /scratch/stefan/7770667/working/building/REAL300020312634 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/212 `/scratch/stefan/7770667/working/3D/212' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC(=O)N2CCOCC2C1) `REAL300020312634.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312634/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312634 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC(=O)N2CCOCC2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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: [12, 12, 6, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 6, 6, 5, 5, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 66 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 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: 108 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312634 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC(=O)N2CCOCC2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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: [25, 25, 14, 6, 6, 6, 6, 18, 27, 38, 38, 38, 38, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 14, 14, 18, 18, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 66 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 221 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312634 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC(=O)N2CCOCC2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 23, 13, 13, 8, 4, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 27, 27, 27, 23, 23, 8, 8, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 29 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 132 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312634 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312634 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312634/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312634/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312634 Building REAL300020312635 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312635' /scratch/stefan/7770667/working/building/REAL300020312635 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312635 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312635/0 /scratch/stefan/7770667/working/building/REAL300020312635 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/213 `/scratch/stefan/7770667/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC(=O)N2CCOCC2C1) `REAL300020312635.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312635 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC(=O)N2CCOCC2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 7, 9, 9, 9, 9, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 5, 5, 7, 7, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 38 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 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: 76 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312635 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC(=O)N2CCOCC2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 12, 5, 5, 5, 5, 14, 20, 20, 20, 20, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 12, 12, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 38 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 126 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312635 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC(=O)N2CCOCC2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 23, 9, 9, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 34, 34, 34, 23, 23, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 38 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 154 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312635 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312635/1 /scratch/stefan/7770667/working/building/REAL300020312635 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/214 `/scratch/stefan/7770667/working/3D/214' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC(=O)N2CCOCC2C1) `REAL300020312635.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312635 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC(=O)N2CCOCC2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 7, 9, 9, 9, 9, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 5, 5, 7, 7, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 38 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 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: 76 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312635 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC(=O)N2CCOCC2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 12, 5, 5, 5, 5, 14, 20, 20, 20, 20, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 12, 12, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 38 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 126 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312635 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC(=O)N2CCOCC2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 1, 11, 8, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 23, 9, 9, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 34, 34, 34, 23, 23, 3, 3, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 38 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 154 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312635 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312635 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312635/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312635/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312635 Building REAL300020312636 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312636' /scratch/stefan/7770667/working/building/REAL300020312636 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312636 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312636/0 /scratch/stefan/7770667/working/building/REAL300020312636 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/215 `/scratch/stefan/7770667/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC2CC(F)(C2)C1) `REAL300020312636.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312636 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC2CC(F)(C2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 12, 6, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 6, 6, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5] 71 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312636 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC2CC(F)(C2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 22, 13, 5, 5, 5, 5, 18, 27, 43, 43, 43, 43, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 13, 13, 18, 18, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1] 71 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312636 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC2CC(F)(C2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 26, 25, 16, 16, 8, 4, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 25, 25, 25, 25, 25, 25, 25, 26, 26, 26, 25, 25, 8, 8, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25] 28 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312636 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312636/1 /scratch/stefan/7770667/working/building/REAL300020312636 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/216 `/scratch/stefan/7770667/working/3D/216' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC2CC(F)(C2)C1) `REAL300020312636.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312636/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312636 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC2CC(F)(C2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 12, 6, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 6, 6, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5] 78 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312636 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC2CC(F)(C2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 13, 5, 5, 5, 5, 18, 27, 43, 43, 43, 43, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 13, 13, 18, 18, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1] 78 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312636 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC2CC(F)(C2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 26, 25, 16, 16, 8, 4, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 25, 25, 25, 25, 25, 25, 25, 26, 26, 26, 25, 25, 8, 8, 4, 4, 25, 25, 25, 25, 25, 25, 25, 25, 25] 28 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312636 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312636 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312636/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312636/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312636 Building REAL300020312637 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312637' /scratch/stefan/7770667/working/building/REAL300020312637 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312637 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312637/0 /scratch/stefan/7770667/working/building/REAL300020312637 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/217 `/scratch/stefan/7770667/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC2CC(F)(C2)C1) `REAL300020312637.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312637 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC2CC(F)(C2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 15, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 35 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 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: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312637 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC2CC(F)(C2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 15, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 12, 5, 5, 5, 5, 13, 19, 19, 19, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 12, 12, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1] 35 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 111 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312637 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC2CC(F)(C2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 15, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 20, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 19, 19, 19, 19, 19, 19, 19, 31, 31, 31, 20, 20, 3, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19] 35 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 147 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312637 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312637/1 /scratch/stefan/7770667/working/building/REAL300020312637 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/218 `/scratch/stefan/7770667/working/3D/218' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC2CC(F)(C2)C1) `REAL300020312637.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312637/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312637 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC2CC(F)(C2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 15, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 35 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 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: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312637 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC2CC(F)(C2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 15, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 12, 5, 5, 5, 5, 13, 19, 19, 19, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 12, 12, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1] 35 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 111 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312637 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC2CC(F)(C2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 15, 5, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 20, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 19, 19, 19, 19, 19, 19, 19, 31, 31, 31, 20, 20, 3, 3, 19, 19, 19, 19, 19, 19, 19, 19, 19] 35 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 147 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312637 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312637 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312637/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312637/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312637 Building REAL300020312638 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312638' /scratch/stefan/7770667/working/building/REAL300020312638 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312638 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312638/0 /scratch/stefan/7770667/working/building/REAL300020312638 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/219 `/scratch/stefan/7770667/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CC2CC(F)(C2)C1) `REAL300020312638.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312638 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CC2CC(F)(C2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 14, 5, 5, 5, 5, 13, 13, 5, 5, 16, 16, 16, 16, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 14, 14, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1] 26 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 19, 20, 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, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 100 number of broken/clashed sets: 6 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312638 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CC2CC(F)(C2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 7, 1, 1, 1, 1, 6, 6, 1, 1, 11, 11, 11, 11, 6, 6, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 7, 7, 6, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5] 26 rigid atoms, others: [3, 4, 5, 6, 17, 18, 19, 20] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 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: 81 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312638 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CC2CC(F)(C2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 20, 11, 11, 1, 1, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 16, 16, 16, 16, 16, 16, 16, 22, 22, 22, 20, 20, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16] 26 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 81 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312638 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1CC2CC(F)(C2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 17, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 21, 21, 21, 17, 17, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13] 26 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 15, 16] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 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]) total number of confs: 87 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312638 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312638/1 /scratch/stefan/7770667/working/building/REAL300020312638 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/220 `/scratch/stefan/7770667/working/3D/220' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CC2CC(F)(C2)C1) `REAL300020312638.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312638/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312638 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CC2CC(F)(C2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 14, 5, 5, 5, 5, 13, 13, 5, 5, 16, 16, 16, 16, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 14, 14, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1] 26 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 19, 20, 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, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 100 number of broken/clashed sets: 6 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312638 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CC2CC(F)(C2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 7, 1, 1, 1, 1, 6, 6, 1, 1, 11, 11, 11, 11, 6, 6, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 13, 13, 13, 7, 7, 6, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5] 26 rigid atoms, others: [3, 4, 5, 6, 17, 18, 19, 20] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 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: 81 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312638 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CC2CC(F)(C2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 20, 11, 11, 1, 1, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 11, 11, 11, 11, 16, 16, 16, 16, 16, 16, 16, 22, 22, 22, 20, 20, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16] 26 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 81 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312638 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1CC2CC(F)(C2)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', '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: [1, 1, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 15, 5, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 17, 6, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 1, 1, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 21, 21, 21, 17, 17, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13] 26 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 15, 16] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 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]) total number of confs: 87 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312638 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312638 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312638/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312638/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312638 Building REAL300020312639 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312639' /scratch/stefan/7770667/working/building/REAL300020312639 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312639 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312639/0 /scratch/stefan/7770667/working/building/REAL300020312639 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/221 `/scratch/stefan/7770667/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1C[C@H]2C[C@@H]1CO2) `REAL300020312639.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312639 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1C[C@H]2C[C@@H]1CO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 7, 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, 7, 7, 7, 7, 7, 7, 7, 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 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 3, 1, 1, 1, 1, 5, 9, 15, 15, 15, 15, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 3, 3, 5, 5, 9, 9, 4, 4, 4, 4, 4, 4] 46 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 86 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312639 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1C[C@H]2C[C@@H]1CO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 7, 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, 7, 7, 7, 7, 7, 7, 7, 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 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 8, 4, 4, 4, 4, 11, 16, 25, 25, 25, 25, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 8, 8, 11, 11, 16, 16, 1, 1, 1, 1, 1, 1] 46 rigid atoms, others: [34, 35, 36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 134 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312639 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1C[C@H]2C[C@@H]1CO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 7, 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, 7, 7, 7, 7, 7, 7, 7, 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 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, 12, 12, 7, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 16, 16, 16, 16, 16, 7, 7, 4, 4, 12, 12, 12, 12, 12, 12] 16 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 62 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312639 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312639/1 /scratch/stefan/7770667/working/building/REAL300020312639 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/222 `/scratch/stefan/7770667/working/3D/222' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1C[C@H]2C[C@@H]1CO2) `REAL300020312639.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312639/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312639 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1C[C@H]2C[C@@H]1CO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 7, 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, 7, 7, 7, 7, 7, 7, 7, 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 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 3, 1, 1, 1, 1, 5, 9, 15, 15, 15, 15, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 3, 3, 5, 5, 9, 9, 4, 4, 4, 4, 4, 4] 46 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 86 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312639 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1C[C@H]2C[C@@H]1CO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 7, 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, 7, 7, 7, 7, 7, 7, 7, 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 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 8, 4, 4, 4, 4, 11, 16, 25, 25, 25, 25, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 8, 8, 11, 11, 16, 16, 1, 1, 1, 1, 1, 1] 46 rigid atoms, others: [34, 35, 36, 37, 38, 39, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 134 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312639 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1C[C@H]2C[C@@H]1CO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 7, 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, 7, 7, 7, 7, 7, 7, 7, 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 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, 12, 12, 7, 4, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 16, 16, 16, 16, 16, 7, 7, 4, 4, 12, 12, 12, 12, 12, 12] 16 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 59 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312639 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312639 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312639/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312639/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312639 Building REAL300020312640 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312640' /scratch/stefan/7770667/working/building/REAL300020312640 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312640 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312640/0 /scratch/stefan/7770667/working/building/REAL300020312640 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/223 `/scratch/stefan/7770667/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1C[C@H]2C[C@@H]1CO2) `REAL300020312640.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312640 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1C[C@H]2C[C@@H]1CO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 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, 7, 7, 7, 7, 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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 3, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 3, 3, 5, 5, 4, 4, 4, 4, 4, 4] 26 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 48 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312640 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1C[C@H]2C[C@@H]1CO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 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, 7, 7, 7, 7, 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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 6, 4, 4, 4, 4, 9, 13, 13, 13, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 6, 6, 9, 9, 1, 1, 1, 1, 1, 1] 26 rigid atoms, others: [32, 33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 64 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312640 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1C[C@H]2C[C@@H]1CO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 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, 7, 7, 7, 7, 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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 16, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 24, 24, 24, 16, 16, 3, 3, 13, 13, 13, 13, 13, 13] 26 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 109 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312640 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312640/1 /scratch/stefan/7770667/working/building/REAL300020312640 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/224 `/scratch/stefan/7770667/working/3D/224' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1C[C@H]2C[C@@H]1CO2) `REAL300020312640.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312640/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312640 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1C[C@H]2C[C@@H]1CO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 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, 7, 7, 7, 7, 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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 3, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 3, 3, 5, 5, 4, 4, 4, 4, 4, 4] 26 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 48 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312640 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1C[C@H]2C[C@@H]1CO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 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, 7, 7, 7, 7, 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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 6, 4, 4, 4, 4, 9, 13, 13, 13, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 6, 6, 9, 9, 1, 1, 1, 1, 1, 1] 26 rigid atoms, others: [32, 33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 64 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312640 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1C[C@H]2C[C@@H]1CO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 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, 7, 7, 7, 7, 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 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 16, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 24, 24, 24, 16, 16, 3, 3, 13, 13, 13, 13, 13, 13] 26 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 109 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312640 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312640 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312640/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312640/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312640 Building REAL300020312641 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312641' /scratch/stefan/7770667/working/building/REAL300020312641 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312641 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312641/0 /scratch/stefan/7770667/working/building/REAL300020312641 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/225 `/scratch/stefan/7770667/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1C[C@H]2C[C@@H]1CO2) `REAL300020312641.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312641 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1C[C@H]2C[C@@H]1CO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', '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, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 8, 4, 4, 4, 4, 8, 8, 5, 5, 8, 8, 8, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1] 15 rigid atoms, others: [38, 39, 40, 41, 42, 43, 19, 20, 21, 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, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 59 number of broken/clashed sets: 2 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312641 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1C[C@H]2C[C@@H]1CO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', '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, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 6, 1, 1, 1, 1, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 6, 6, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4] 15 rigid atoms, others: [3, 4, 5, 6, 17, 18, 19, 20] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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: 60 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312641 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1C[C@H]2C[C@@H]1CO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', '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, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 11, 5, 5, 2, 2, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 14, 11, 11, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8] 15 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 71 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312641 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1C[C@H]2C[C@@H]1CO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', '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, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 11, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 14, 11, 11, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8] 15 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 15, 16, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43]) total number of confs: 59 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312641 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312641/1 /scratch/stefan/7770667/working/building/REAL300020312641 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/226 `/scratch/stefan/7770667/working/3D/226' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1C[C@H]2C[C@@H]1CO2) `REAL300020312641.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312641/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312641 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1C[C@H]2C[C@@H]1CO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', '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, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 8, 4, 4, 4, 4, 8, 8, 6, 6, 8, 8, 8, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1] 15 rigid atoms, others: [38, 39, 40, 41, 42, 43, 19, 20, 21, 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, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 60 number of broken/clashed sets: 2 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312641 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1C[C@H]2C[C@@H]1CO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', '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, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 6, 1, 1, 1, 1, 5, 5, 3, 3, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 6, 6, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4] 15 rigid atoms, others: [3, 4, 5, 6, 17, 18, 19, 20] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 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: 59 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312641 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1C[C@H]2C[C@@H]1CO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', '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, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 11, 5, 5, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 14, 11, 11, 4, 4, 4, 4, 8, 8, 8, 8, 8, 8] 15 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 72 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312641 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1C[C@H]2C[C@@H]1CO2 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'O.3', '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, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 7, 5, 5, 7, 5, 12, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 11, 5, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 1, 1, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 14, 11, 11, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8] 15 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 15, 16, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43]) total number of confs: 59 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312641 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312641 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312641/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312641/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312641 Building REAL300020312642 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312642' /scratch/stefan/7770667/working/building/REAL300020312642 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312642 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312642/0 /scratch/stefan/7770667/working/building/REAL300020312642 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/227 `/scratch/stefan/7770667/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(CNC(=O)N2)CC1) `REAL300020312642.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312642 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(CNC(=O)N2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [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, 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: [12, 12, 6, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 6, 6, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 65 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 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: 107 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312642 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(CNC(=O)N2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [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, 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: [25, 25, 13, 5, 5, 5, 5, 18, 27, 34, 34, 34, 34, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 13, 13, 18, 18, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 65 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 224 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312642 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC2(CNC(=O)N2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [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, 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: [24, 24, 21, 13, 13, 8, 4, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 24, 24, 24, 21, 21, 8, 8, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 25 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 114 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312642 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312642/1 /scratch/stefan/7770667/working/building/REAL300020312642 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/228 `/scratch/stefan/7770667/working/3D/228' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(CNC(=O)N2)CC1) `REAL300020312642.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312642/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312642 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(CNC(=O)N2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [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, 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: [12, 12, 6, 1, 1, 1, 1, 5, 9, 16, 16, 16, 16, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 6, 6, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 65 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 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: 107 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312642 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(CNC(=O)N2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [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, 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: [25, 25, 13, 5, 5, 5, 5, 18, 27, 34, 34, 34, 34, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 13, 13, 18, 18, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 65 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 224 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312642 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC2(CNC(=O)N2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [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, 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: [24, 24, 21, 13, 13, 8, 4, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 24, 24, 24, 21, 21, 8, 8, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 25 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 114 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312642 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312642 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312642/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312642/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312642 Building REAL300020312643 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312643' /scratch/stefan/7770667/working/building/REAL300020312643 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312643 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312643/0 /scratch/stefan/7770667/working/building/REAL300020312643 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/229 `/scratch/stefan/7770667/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(CNC(=O)N2)CC1) `REAL300020312643.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312643 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(CNC(=O)N2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [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, 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: [11, 11, 5, 1, 1, 1, 1, 7, 9, 9, 9, 9, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 5, 5, 7, 7, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 42 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 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: 76 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312643 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(CNC(=O)N2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [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, 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: [20, 20, 12, 5, 5, 5, 5, 15, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 12, 12, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 42 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 132 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312643 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC2(CNC(=O)N2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [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, 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: [36, 36, 23, 9, 9, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 36, 36, 36, 23, 23, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 42 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 170 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312643 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312643/1 /scratch/stefan/7770667/working/building/REAL300020312643 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/230 `/scratch/stefan/7770667/working/3D/230' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(CNC(=O)N2)CC1) `REAL300020312643.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312643 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(CNC(=O)N2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [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, 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: [11, 11, 5, 1, 1, 1, 1, 7, 9, 9, 9, 9, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 5, 5, 7, 7, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 42 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 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: 76 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312643 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(CNC(=O)N2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [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, 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: [20, 20, 12, 5, 5, 5, 5, 15, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 12, 12, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 42 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 132 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312643 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC2(CNC(=O)N2)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [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, 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: [36, 36, 23, 9, 9, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 36, 36, 36, 23, 23, 3, 3, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 42 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 170 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312643 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312643 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312643/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312643/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312643 Building REAL300020312644 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312644' /scratch/stefan/7770667/working/building/REAL300020312644 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312644 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312644/0 /scratch/stefan/7770667/working/building/REAL300020312644 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/231 `/scratch/stefan/7770667/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC[C@@H](C(=O)OC)[C@H](F)C1) `REAL300020312644.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312644 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC[C@@H](C(=O)OC)[C@H](F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 7, 1, 11, 12, 5, 5, 7, 15, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 6, 10, 13, 13, 13, 13, 1, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 10, 4, 4, 4, 4, 5, 5, 5, 5, 5, 6, 6, 10, 10, 4, 4, 4, 4, 10, 10, 10, 4, 4] 43 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 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: 86 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312644 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC[C@@H](C(=O)OC)[C@H](F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 7, 1, 11, 12, 5, 5, 7, 15, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 4, 4, 4, 4, 14, 17, 18, 18, 18, 18, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 9, 9, 9, 9, 9, 14, 14, 17, 17, 1, 1, 1, 1, 4, 4, 4, 1, 1] 43 rigid atoms, others: [38, 39, 40, 41, 45, 46, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312644 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CC[C@@H](C(=O)OC)[C@H](F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 7, 1, 11, 12, 5, 5, 7, 15, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 23, 13, 13, 8, 4, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 22, 22, 22, 22, 22, 55, 55, 55, 22, 22, 22, 22, 24, 24, 24, 23, 23, 8, 8, 4, 4, 22, 22, 22, 22, 55, 55, 55, 22, 22] 64 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 219 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312644 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312644/1 /scratch/stefan/7770667/working/building/REAL300020312644 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/232 `/scratch/stefan/7770667/working/3D/232' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC[C@@H](C(=O)OC)[C@H](F)C1) `REAL300020312644.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312644/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312644 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC[C@@H](C(=O)OC)[C@H](F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 7, 1, 11, 12, 5, 5, 7, 15, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 1, 1, 1, 1, 6, 10, 13, 13, 13, 13, 1, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 10, 4, 4, 4, 4, 5, 5, 5, 5, 5, 6, 6, 10, 10, 4, 4, 4, 4, 10, 10, 10, 4, 4] 42 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 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: 86 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312644 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC[C@@H](C(=O)OC)[C@H](F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 7, 1, 11, 12, 5, 5, 7, 15, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 4, 4, 4, 4, 14, 17, 18, 18, 18, 18, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 1, 9, 9, 9, 9, 9, 14, 14, 17, 17, 1, 1, 1, 1, 4, 4, 4, 1, 1] 42 rigid atoms, others: [38, 39, 40, 41, 45, 46, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312644 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CC[C@@H](C(=O)OC)[C@H](F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 7, 1, 11, 12, 5, 5, 7, 15, 5, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 23, 13, 13, 8, 4, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 22, 22, 22, 22, 22, 55, 55, 55, 22, 22, 22, 22, 24, 24, 24, 23, 23, 8, 8, 4, 4, 22, 22, 22, 22, 55, 55, 55, 22, 22] 64 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 219 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312644 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312644 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312644/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312644/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312644 Building REAL300020312645 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312645' /scratch/stefan/7770667/working/building/REAL300020312645 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312645 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312645/0 /scratch/stefan/7770667/working/building/REAL300020312645 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/233 `/scratch/stefan/7770667/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC[C@@H](C(=O)OC)[C@H](F)C1) `REAL300020312645.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312645 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC[C@@H](C(=O)OC)[C@H](F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 7, 1, 11, 12, 5, 5, 7, 15, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 6, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 11, 5, 5, 5, 5, 12, 12, 12, 6, 6, 6, 6, 5, 5, 5, 5, 11, 11, 11, 5, 5] 99 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 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: 94 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312645 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC[C@@H](C(=O)OC)[C@H](F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 7, 1, 11, 12, 5, 5, 7, 15, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 13, 5, 5, 5, 5, 15, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 19, 19, 19, 13, 13, 15, 15, 1, 1, 1, 1, 4, 4, 4, 1, 1] 99 rigid atoms, others: [35, 36, 37, 38, 42, 43, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41]) total number of confs: 132 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312645 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CC[C@@H](C(=O)OC)[C@H](F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 7, 1, 11, 12, 5, 5, 7, 15, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 24, 8, 8, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 20, 20, 20, 20, 20, 43, 43, 43, 20, 20, 20, 20, 35, 35, 35, 24, 24, 3, 3, 20, 20, 20, 20, 43, 43, 43, 20, 20] 89 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 230 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312645 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312645/1 /scratch/stefan/7770667/working/building/REAL300020312645 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/234 `/scratch/stefan/7770667/working/3D/234' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC[C@@H](C(=O)OC)[C@H](F)C1) `REAL300020312645.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312645 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC[C@@H](C(=O)OC)[C@H](F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 7, 1, 11, 12, 5, 5, 7, 15, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 6, 1, 1, 1, 1, 6, 8, 8, 8, 8, 1, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 11, 5, 5, 5, 5, 12, 12, 12, 6, 6, 6, 6, 5, 5, 5, 5, 11, 11, 11, 5, 5] 99 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 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: 94 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312645 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC[C@@H](C(=O)OC)[C@H](F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 7, 1, 11, 12, 5, 5, 7, 15, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 13, 5, 5, 5, 5, 15, 21, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 19, 19, 19, 13, 13, 15, 15, 1, 1, 1, 1, 4, 4, 4, 1, 1] 99 rigid atoms, others: [35, 36, 37, 38, 42, 43, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41]) total number of confs: 132 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312645 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CC[C@@H](C(=O)OC)[C@H](F)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'H', 'F', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 7, 1, 11, 12, 5, 5, 7, 15, 5, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 24, 8, 8, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 20, 20, 20, 20, 20, 43, 43, 43, 20, 20, 20, 20, 35, 35, 35, 24, 24, 3, 3, 20, 20, 20, 20, 43, 43, 43, 20, 20] 89 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 230 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312645 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312645 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312645/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312645/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312645 Building REAL300020312646 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312646' /scratch/stefan/7770667/working/building/REAL300020312646 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312646 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312646/0 /scratch/stefan/7770667/working/building/REAL300020312646 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/235 `/scratch/stefan/7770667/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(COCC(=O)OC)CC1) `REAL300020312646.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312646 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(COCC(=O)OC)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 1, 11, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 5, 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, 5, 1, 1, 1, 1, 2, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4, 16, 30, 78, 144, 144, 144, 4, 4, 6, 6, 6, 5, 5, 2, 2, 4, 4, 4, 4, 4, 16, 16, 78, 78, 143, 144, 144, 4, 4, 4, 4] 201 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312646 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(COCC(=O)OC)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 1, 11, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 5, 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: [10, 10, 9, 4, 4, 4, 4, 7, 13, 13, 13, 13, 4, 4, 1, 1, 1, 1, 1, 1, 6, 12, 36, 83, 83, 83, 1, 1, 10, 10, 10, 9, 9, 7, 7, 1, 1, 1, 1, 1, 6, 6, 36, 36, 82, 83, 83, 1, 1, 1, 1] 201 rigid atoms, others: [48, 35, 36, 37, 38, 39, 47, 50, 14, 15, 16, 17, 18, 19, 49, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312646 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(COCC(=O)OC)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 1, 11, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 5, 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: [15, 15, 14, 5, 5, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 14, 14, 14, 14, 38, 73, 149, 193, 193, 193, 14, 14, 15, 15, 15, 14, 14, 4, 4, 14, 14, 14, 14, 14, 38, 38, 149, 149, 193, 193, 193, 14, 14, 14, 14] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 771 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312646 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312646/1 /scratch/stefan/7770667/working/building/REAL300020312646 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/236 `/scratch/stefan/7770667/working/3D/236' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(COCC(=O)OC)CC1) `REAL300020312646.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312646/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312646 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(COCC(=O)OC)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 1, 11, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 5, 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, 5, 1, 1, 1, 1, 2, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4, 16, 30, 79, 147, 147, 147, 4, 4, 6, 6, 6, 5, 5, 2, 2, 4, 4, 4, 4, 4, 16, 16, 79, 79, 146, 147, 147, 4, 4, 4, 4] 201 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312646 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(COCC(=O)OC)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 1, 11, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 5, 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: [10, 10, 9, 4, 4, 4, 4, 7, 13, 13, 13, 13, 4, 4, 1, 1, 1, 1, 1, 1, 6, 12, 38, 93, 93, 93, 1, 1, 10, 10, 10, 9, 9, 7, 7, 1, 1, 1, 1, 1, 6, 6, 38, 38, 92, 93, 93, 1, 1, 1, 1] 201 rigid atoms, others: [48, 35, 36, 37, 38, 39, 47, 50, 14, 15, 16, 17, 18, 19, 49, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 358 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312646 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(COCC(=O)OC)CC1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 12, 5, 1, 11, 12, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 5, 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: [14, 14, 13, 4, 4, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 13, 13, 13, 13, 39, 72, 155, 192, 192, 192, 13, 13, 14, 14, 14, 13, 13, 3, 3, 13, 13, 13, 13, 13, 39, 39, 155, 155, 192, 192, 192, 13, 13, 13, 13] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 767 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312646 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312646 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312646/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312646/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312646 Building REAL300020312647 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312647' /scratch/stefan/7770667/working/building/REAL300020312647 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312647 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312647/0 /scratch/stefan/7770667/working/building/REAL300020312647 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/237 `/scratch/stefan/7770667/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1NC1=NN(CC(C)C)C=C1) `REAL300020312647.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312647 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1NC1=NN(CC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 5, 7, 12, 12, 12, 12, 1, 1, 1, 1, 7, 14, 14, 14, 40, 48, 48, 14, 14, 5, 5, 5, 3, 3, 5, 5, 7, 7, 7, 40, 40, 48, 48, 48, 48, 48, 48, 48, 14, 14] 201 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 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: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312647 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1NC1=NN(CC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 14, 14, 14, 14, 52, 57, 78, 78, 78, 78, 14, 14, 4, 1, 1, 1, 1, 1, 5, 7, 7, 1, 1, 38, 38, 38, 25, 25, 52, 52, 57, 57, 4, 5, 5, 7, 7, 7, 7, 7, 7, 7, 1, 1] 201 rigid atoms, others: [45, 46, 16, 17, 18, 19, 20, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312647 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1NC1=NN(CC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 47, 78, 78, 78, 156, 170, 170, 78, 78, 35, 35, 35, 23, 23, 6, 6, 4, 4, 47, 156, 156, 170, 170, 170, 170, 170, 170, 170, 78, 78] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 759 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312647 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312647/1 /scratch/stefan/7770667/working/building/REAL300020312647 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/238 `/scratch/stefan/7770667/working/3D/238' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1NC1=NN(CC(C)C)C=C1) `REAL300020312647.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312647/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312647 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1NC1=NN(CC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 5, 7, 12, 12, 12, 12, 1, 1, 1, 1, 7, 14, 14, 14, 40, 48, 48, 14, 14, 5, 5, 5, 3, 3, 5, 5, 7, 7, 7, 40, 40, 48, 48, 48, 48, 48, 48, 48, 14, 14] 201 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 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: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312647 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1NC1=NN(CC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 14, 14, 14, 14, 52, 57, 78, 78, 78, 78, 14, 14, 4, 1, 1, 1, 1, 1, 5, 7, 7, 1, 1, 38, 38, 38, 25, 25, 52, 52, 57, 57, 4, 5, 5, 7, 7, 7, 7, 7, 7, 7, 1, 1] 201 rigid atoms, others: [45, 46, 16, 17, 18, 19, 20, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 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: 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312647 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1NC1=NN(CC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 8, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 13, 13, 6, 4, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 46, 78, 78, 78, 156, 170, 170, 78, 78, 34, 34, 34, 22, 22, 6, 6, 4, 4, 46, 156, 156, 170, 170, 170, 170, 170, 170, 170, 78, 78] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 760 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312647 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312647 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312647/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312647/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312647 Building REAL300020312648 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312648' /scratch/stefan/7770667/working/building/REAL300020312648 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312648 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312648/0 /scratch/stefan/7770667/working/building/REAL300020312648 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/239 `/scratch/stefan/7770667/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1NC1=NN(CC(C)C)C=C1) `REAL300020312648.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312648 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1NC1=NN(CC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 8, 8, 5, 5, 5, 5, 1, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [6, 6, 3, 1, 1, 1, 1, 2, 4, 4, 4, 4, 1, 1, 1, 1, 9, 19, 19, 19, 42, 47, 47, 19, 19, 6, 7, 7, 2, 2, 2, 2, 9, 42, 42, 47, 47, 47, 47, 47, 47, 47, 19, 19] 201 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312648 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1NC1=NN(CC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 8, 8, 5, 5, 5, 5, 1, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 19, 19, 19, 19, 37, 55, 55, 55, 55, 19, 19, 5, 1, 1, 1, 1, 1, 5, 7, 7, 1, 1, 49, 49, 49, 34, 34, 37, 37, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 1, 1] 201 rigid atoms, others: [42, 43, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 358 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312648 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1NC1=NN(CC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 8, 8, 5, 5, 5, 5, 1, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 4, 4, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 24, 55, 55, 55, 91, 91, 91, 55, 55, 15, 15, 15, 8, 8, 3, 3, 24, 91, 91, 91, 91, 91, 91, 91, 91, 91, 55, 55] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 353 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312648 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312648/1 /scratch/stefan/7770667/working/building/REAL300020312648 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/240 `/scratch/stefan/7770667/working/3D/240' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1NC1=NN(CC(C)C)C=C1) `REAL300020312648.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312648/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312648 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1NC1=NN(CC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 8, 8, 5, 5, 5, 5, 1, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 1, 1, 1, 1, 9, 19, 19, 19, 42, 47, 47, 19, 19, 7, 7, 7, 2, 2, 2, 2, 9, 42, 42, 47, 47, 47, 47, 47, 47, 47, 19, 19] 201 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312648 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1NC1=NN(CC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 8, 8, 5, 5, 5, 5, 1, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 19, 19, 19, 19, 37, 55, 55, 55, 55, 19, 19, 5, 1, 1, 1, 1, 1, 5, 7, 7, 1, 1, 49, 49, 49, 34, 34, 37, 37, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 1, 1] 201 rigid atoms, others: [42, 43, 15, 16, 17, 18, 19, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 358 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312648 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1NC1=NN(CC(C)C)C=C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', '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'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 1, 8, 8, 5, 5, 5, 5, 1, 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, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 4, 4, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 24, 55, 55, 55, 91, 91, 91, 55, 55, 15, 15, 15, 8, 8, 3, 3, 24, 91, 91, 91, 91, 91, 91, 91, 91, 91, 55, 55] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 353 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312648 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312648 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312648/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312648/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312648 Building REAL300020312649 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312649' /scratch/stefan/7770667/working/building/REAL300020312649 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312649 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312649/0 /scratch/stefan/7770667/working/building/REAL300020312649 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/241 `/scratch/stefan/7770667/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(CNC(C)=O)C1) `REAL300020312649.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312649 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(CNC(C)=O)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 5, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [7, 7, 4, 1, 1, 1, 1, 5, 7, 12, 12, 12, 12, 1, 1, 1, 1, 6, 6, 6, 6, 30, 78, 78, 78, 6, 7, 7, 7, 4, 4, 5, 5, 7, 7, 6, 6, 6, 6, 6, 30, 30, 78, 78, 78, 78, 6, 6] 201 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 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.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312649 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(CNC(C)=O)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 5, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [14, 14, 11, 6, 6, 6, 6, 21, 26, 41, 41, 41, 41, 6, 6, 1, 1, 1, 1, 1, 1, 9, 31, 31, 31, 1, 14, 14, 14, 11, 11, 21, 21, 26, 26, 1, 1, 1, 1, 1, 9, 9, 31, 31, 31, 31, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 46, 15, 16, 17, 18, 19, 20, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312649 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1CCC(CNC(C)=O)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 5, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 26, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 42, 42, 42, 42, 137, 188, 188, 188, 42, 28, 28, 28, 26, 26, 6, 6, 4, 4, 42, 42, 42, 42, 42, 137, 137, 188, 188, 188, 188, 42, 42] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 733 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312649 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312649/1 /scratch/stefan/7770667/working/building/REAL300020312649 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/242 `/scratch/stefan/7770667/working/3D/242' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(CNC(C)=O)C1) `REAL300020312649.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312649/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312649 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(CNC(C)=O)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 5, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [7, 7, 4, 1, 1, 1, 1, 5, 7, 12, 12, 12, 12, 1, 1, 1, 1, 6, 6, 6, 6, 30, 79, 79, 79, 6, 7, 7, 7, 4, 4, 5, 5, 7, 7, 6, 6, 6, 6, 6, 30, 30, 79, 79, 79, 79, 6, 6] 201 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312649 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(CNC(C)=O)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 5, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [14, 14, 11, 6, 6, 6, 6, 21, 26, 41, 41, 41, 41, 6, 6, 1, 1, 1, 1, 1, 1, 9, 31, 31, 31, 1, 14, 14, 14, 11, 11, 21, 21, 26, 26, 1, 1, 1, 1, 1, 9, 9, 31, 31, 31, 31, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 46, 15, 16, 17, 18, 19, 20, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312649 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1CCC(CNC(C)=O)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', '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: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 5, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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, 26, 14, 14, 6, 4, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 42, 42, 42, 42, 137, 188, 188, 188, 42, 28, 28, 28, 26, 26, 6, 6, 4, 4, 42, 42, 42, 42, 42, 137, 137, 188, 188, 188, 188, 42, 42] 201 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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]) total number of confs: 733 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312649 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312649 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312649/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312649/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312649 Building REAL300020312650 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312650' /scratch/stefan/7770667/working/building/REAL300020312650 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312650 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312650/0 /scratch/stefan/7770667/working/building/REAL300020312650 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/243 `/scratch/stefan/7770667/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(CNC(C)=O)C1) `REAL300020312650.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312650 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(CNC(C)=O)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 5, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [11, 11, 5, 1, 1, 1, 1, 2, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 6, 37, 98, 98, 98, 6, 11, 11, 11, 5, 5, 2, 2, 6, 6, 6, 6, 6, 37, 37, 98, 98, 98, 98, 6, 6] 201 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 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: 344 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312650 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(CNC(C)=O)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 5, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [22, 22, 14, 6, 6, 6, 6, 9, 17, 17, 17, 17, 6, 6, 1, 1, 1, 1, 1, 1, 10, 38, 38, 38, 1, 22, 22, 22, 14, 14, 9, 9, 1, 1, 1, 1, 1, 10, 10, 38, 38, 38, 38, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 43, 44, 14, 15, 16, 17, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312650 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1CCC(CNC(C)=O)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 5, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [20, 20, 13, 4, 4, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 17, 17, 17, 17, 97, 168, 168, 168, 17, 20, 20, 20, 13, 13, 3, 3, 17, 17, 17, 17, 17, 97, 97, 168, 168, 168, 168, 17, 17] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 623 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312650 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312650/1 /scratch/stefan/7770667/working/building/REAL300020312650 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/244 `/scratch/stefan/7770667/working/3D/244' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(CNC(C)=O)C1) `REAL300020312650.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312650 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(CNC(C)=O)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 5, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [11, 11, 5, 1, 1, 1, 1, 2, 4, 4, 4, 4, 1, 1, 1, 1, 6, 6, 6, 6, 37, 99, 99, 99, 6, 11, 11, 11, 5, 5, 2, 2, 6, 6, 6, 6, 6, 37, 37, 99, 99, 99, 99, 6, 6] 201 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 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: 346 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312650 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(CNC(C)=O)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 5, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [22, 22, 14, 6, 6, 6, 6, 9, 17, 17, 17, 17, 6, 6, 1, 1, 1, 1, 1, 1, 10, 38, 38, 38, 1, 22, 22, 22, 14, 14, 9, 9, 1, 1, 1, 1, 1, 10, 10, 38, 38, 38, 38, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 43, 44, 14, 15, 16, 17, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312650 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1CCC(CNC(C)=O)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.3', 'O.2', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 8, 1, 5, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 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: [20, 20, 13, 4, 4, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 17, 17, 17, 17, 95, 168, 168, 168, 17, 20, 20, 20, 13, 13, 3, 3, 17, 17, 17, 17, 17, 95, 95, 168, 168, 168, 168, 17, 17] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 625 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312650 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312650 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312650/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312650/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312650 Building REAL300020312651 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312651' /scratch/stefan/7770667/working/building/REAL300020312651 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312651 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312651/0 /scratch/stefan/7770667/working/building/REAL300020312651 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/245 `/scratch/stefan/7770667/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1C[C@H]2OCCO[C@H]2C1) `REAL300020312651.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312651 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1C[C@H]2OCCO[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 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, 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 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 5, 9, 15, 15, 15, 15, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 5, 5, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5] 76 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 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: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312651 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1C[C@H]2OCCO[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 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, 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 76 conformations in input total number of sets (complete confs): 76 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 16, 5, 5, 5, 5, 22, 34, 40, 40, 40, 40, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 16, 16, 22, 22, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1] 76 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312651 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1C[C@H]2OCCO[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 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, 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 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 9, 9, 5, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 15, 15, 15, 15, 15, 5, 5, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18] 23 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 70 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312651 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312651/1 /scratch/stefan/7770667/working/building/REAL300020312651 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/246 `/scratch/stefan/7770667/working/3D/246' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1C[C@H]2OCCO[C@H]2C1) `REAL300020312651.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312651/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312651 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1C[C@H]2OCCO[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 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, 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 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 5, 1, 1, 1, 1, 5, 9, 15, 15, 15, 15, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 5, 5, 5, 5, 9, 9, 5, 5, 5, 5, 5, 5, 5, 5] 78 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 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: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312651 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1C[C@H]2OCCO[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 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, 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 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 16, 5, 5, 5, 5, 22, 34, 40, 40, 40, 40, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 16, 16, 22, 22, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1] 78 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312651 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1C[C@H]2OCCO[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 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, 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 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 10, 10, 6, 4, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 16, 16, 16, 16, 16, 6, 6, 4, 4, 20, 20, 20, 20, 20, 20, 20, 20] 24 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312651 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312651 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312651/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312651/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312651 Building REAL300020312652 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312652' /scratch/stefan/7770667/working/building/REAL300020312652 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312652 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312652/0 /scratch/stefan/7770667/working/building/REAL300020312652 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/247 `/scratch/stefan/7770667/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1C[C@H]2OCCO[C@H]2C1) `REAL300020312652.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312652 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1C[C@H]2OCCO[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 12, 5, 7, 5, 7, 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, 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] 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: [11, 11, 5, 1, 1, 1, 1, 7, 9, 9, 9, 9, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 5, 5, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6] 49 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 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: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312652 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1C[C@H]2OCCO[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 12, 5, 7, 5, 7, 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, 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] 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: [24, 24, 15, 6, 6, 6, 6, 17, 25, 25, 25, 25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 15, 15, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1] 49 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 152 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312652 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1C[C@H]2OCCO[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 12, 5, 7, 5, 7, 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, 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] 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: [36, 36, 23, 9, 9, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 36, 36, 36, 23, 23, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25] 49 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 168 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312652 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312652/1 /scratch/stefan/7770667/working/building/REAL300020312652 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/248 `/scratch/stefan/7770667/working/3D/248' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1C[C@H]2OCCO[C@H]2C1) `REAL300020312652.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312652 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1C[C@H]2OCCO[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 12, 5, 7, 5, 7, 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, 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] 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: [11, 11, 5, 1, 1, 1, 1, 7, 9, 9, 9, 9, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 5, 5, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6] 49 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 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: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312652 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1C[C@H]2OCCO[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 12, 5, 7, 5, 7, 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, 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] 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: [24, 24, 15, 6, 6, 6, 6, 17, 25, 25, 25, 25, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 15, 15, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1] 49 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 32, 26, 27, 28, 29, 30, 31]) total number of confs: 152 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312652 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1C[C@H]2OCCO[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 12, 5, 7, 5, 7, 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, 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] 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: [36, 36, 23, 9, 9, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 36, 36, 36, 23, 23, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25] 49 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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]) total number of confs: 168 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312652 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312652 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312652/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312652/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312652 Building REAL300020312653 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312653' /scratch/stefan/7770667/working/building/REAL300020312653 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312653 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312653/0 /scratch/stefan/7770667/working/building/REAL300020312653 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/249 `/scratch/stefan/7770667/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1C[C@H]2OCCO[C@H]2C1) `REAL300020312653.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312653 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1C[C@H]2OCCO[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 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, 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 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 18, 6, 6, 6, 6, 14, 14, 11, 14, 14, 14, 14, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 18, 18, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1] 27 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 19, 20, 21, 22, 23, 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, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 98 number of broken/clashed sets: 5 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312653 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1C[C@H]2OCCO[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 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, 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 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 8, 1, 1, 1, 1, 5, 5, 3, 5, 6, 6, 6, 6, 5, 5, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 8, 8, 5, 5, 5, 5, 6, 6, 5, 6, 6, 6, 6, 6] 27 rigid atoms, others: [3, 4, 5, 6, 17, 18, 19, 20] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 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: 79 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312653 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1C[C@H]2OCCO[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 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, 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 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 17, 6, 6, 2, 1, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 19, 19, 19, 17, 17, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14] 27 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 81 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312653 none C#CCCN1C(C2=CC=C(C3=N[N-]N=N3)C=C2)=NN=C1N1C[C@H]2OCCO[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 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, 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 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 16, 5, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 18, 18, 18, 16, 16, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14] 27 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 39, 15, 16, 38, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 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]) total number of confs: 75 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312653 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312653/1 /scratch/stefan/7770667/working/building/REAL300020312653 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/250 `/scratch/stefan/7770667/working/3D/250' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1C[C@H]2OCCO[C@H]2C1) `REAL300020312653.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312653/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312653 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1C[C@H]2OCCO[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 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, 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 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 18, 6, 6, 6, 6, 14, 14, 11, 14, 14, 14, 14, 14, 14, 14, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 18, 18, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1] 27 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 19, 20, 21, 22, 23, 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, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 98 number of broken/clashed sets: 5 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312653 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1C[C@H]2OCCO[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 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, 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 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 8, 1, 1, 1, 1, 5, 5, 2, 4, 6, 6, 6, 6, 5, 5, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 8, 8, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6] 27 rigid atoms, others: [3, 4, 5, 6, 17, 18, 19, 20] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 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: 81 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312653 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1C[C@H]2OCCO[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 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, 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 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 17, 6, 6, 3, 2, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 19, 19, 19, 17, 17, 3, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14] 27 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 79 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312653 none C#CCCN1C(C2=CC=C(C3=NN=N[N-]3)C=C2)=NN=C1N1C[C@H]2OCCO[C@H]2C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', '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, 1, 1, 1, 8, 8, 8, 8, 1, 1, 8, 8, 1, 8, 5, 5, 7, 12, 5, 5, 12, 5, 7, 5, 7, 7, 7, 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, 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 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 16, 5, 5, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 1, 1, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 18, 18, 18, 16, 16, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14] 27 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 39, 15, 16, 38, 37] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 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]) total number of confs: 75 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312653 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312653 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312653/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312653/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312653 Building REAL300020312654 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312654' /scratch/stefan/7770667/working/building/REAL300020312654 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312654 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312654/0 /scratch/stefan/7770667/working/building/REAL300020312654 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/251 `/scratch/stefan/7770667/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1C[C@@H](C(=O)OC)[C@H](C(C)C)C1) `REAL300020312654.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312654 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1C[C@@H](C(=O)OC)[C@H](C(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 1, 11, 12, 5, 5, 7, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 4, 1, 1, 1, 1, 5, 8, 8, 8, 8, 8, 1, 1, 1, 1, 5, 5, 5, 5, 13, 13, 13, 5, 5, 5, 7, 7, 5, 7, 7, 7, 4, 4, 5, 5, 8, 8, 5, 5, 13, 13, 13, 7, 7, 7, 7, 7, 7, 7, 5, 5] 58 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312654 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1C[C@@H](C(=O)OC)[C@H](C(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 1, 11, 12, 5, 5, 7, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 14, 5, 5, 5, 5, 14, 19, 19, 19, 19, 19, 5, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 3, 3, 1, 17, 17, 17, 14, 14, 14, 14, 19, 19, 1, 1, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 1, 1] 58 rigid atoms, others: [51, 39, 40, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 155 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312654 none C#CCCN1C(CCC2=N[N-]N=N2)=NN=C1N1C[C@@H](C(=O)OC)[C@H](C(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 1, 11, 12, 5, 5, 7, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 14, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 19, 19, 19, 19, 36, 36, 36, 19, 19, 19, 20, 20, 19, 17, 17, 17, 14, 14, 5, 5, 3, 3, 19, 19, 36, 36, 36, 20, 20, 20, 20, 20, 20, 20, 19, 19] 58 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 153 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312654 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312654/1 /scratch/stefan/7770667/working/building/REAL300020312654 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/252 `/scratch/stefan/7770667/working/3D/252' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1C[C@@H](C(=O)OC)[C@H](C(C)C)C1) `REAL300020312654.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312654 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1C[C@@H](C(=O)OC)[C@H](C(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 1, 11, 12, 5, 5, 7, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [7, 7, 4, 1, 1, 1, 1, 5, 8, 8, 8, 8, 8, 1, 1, 1, 1, 5, 5, 5, 5, 13, 13, 13, 5, 5, 5, 7, 7, 5, 7, 7, 7, 4, 4, 5, 5, 8, 8, 5, 5, 13, 13, 13, 7, 7, 7, 7, 7, 7, 7, 5, 5] 58 rigid atoms, others: [3, 4, 5, 6, 13, 14, 15, 16] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312654 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1C[C@@H](C(=O)OC)[C@H](C(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 1, 11, 12, 5, 5, 7, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 14, 5, 5, 5, 5, 14, 19, 19, 19, 19, 19, 5, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 3, 3, 1, 17, 17, 17, 14, 14, 14, 14, 19, 19, 1, 1, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 1, 1] 58 rigid atoms, others: [51, 39, 40, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 155 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312654 none C#CCCN1C(CCC2=NN=N[N-]2)=NN=C1N1C[C@@H](C(=O)OC)[C@H](C(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 1, 11, 12, 5, 5, 7, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 14, 10, 10, 5, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 19, 19, 19, 19, 36, 36, 36, 19, 19, 19, 20, 20, 19, 17, 17, 17, 14, 14, 5, 5, 3, 3, 19, 19, 36, 36, 36, 20, 20, 20, 20, 20, 20, 20, 19, 19] 58 rigid atoms, others: [7, 8, 9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 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: 153 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312654 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312654 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312654/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312654/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312654 Building REAL300020312655 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312655' /scratch/stefan/7770667/working/building/REAL300020312655 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312655 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312655/0 /scratch/stefan/7770667/working/building/REAL300020312655 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/253 `/scratch/stefan/7770667/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1C[C@@H](C(=O)OC)[C@H](C(C)C)C1) `REAL300020312655.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312655 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1C[C@@H](C(=O)OC)[C@H](C(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 1, 11, 12, 5, 5, 7, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 4, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 1, 1, 5, 5, 5, 5, 15, 15, 15, 5, 5, 5, 8, 8, 5, 10, 10, 10, 4, 4, 5, 5, 5, 5, 15, 15, 15, 8, 8, 8, 8, 8, 8, 8, 5, 5] 113 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 115 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312655 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1C[C@@H](C(=O)OC)[C@H](C(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 1, 11, 12, 5, 5, 7, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 16, 5, 5, 5, 5, 16, 23, 23, 23, 23, 5, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 3, 3, 1, 29, 29, 29, 16, 16, 16, 16, 1, 1, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 1, 1] 113 rigid atoms, others: [48, 36, 37, 49, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 26, 27, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 205 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312655 none C#CCCN1C(CC2=N[N-]N=N2)=NN=C1N1C[C@@H](C(=O)OC)[C@H](C(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 1, 11, 12, 5, 5, 7, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 21, 8, 8, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 24, 24, 24, 24, 52, 52, 52, 24, 24, 24, 26, 26, 24, 31, 31, 31, 21, 21, 4, 4, 24, 24, 52, 52, 52, 26, 26, 26, 26, 26, 26, 26, 24, 24] 113 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 259 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312655 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312655/1 /scratch/stefan/7770667/working/building/REAL300020312655 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/254 `/scratch/stefan/7770667/working/3D/254' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1C[C@@H](C(=O)OC)[C@H](C(C)C)C1) `REAL300020312655.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312655 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1C[C@@H](C(=O)OC)[C@H](C(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 1, 11, 12, 5, 5, 7, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [10, 10, 4, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 1, 1, 5, 5, 5, 5, 15, 15, 15, 5, 5, 5, 8, 8, 5, 10, 10, 10, 4, 4, 5, 5, 5, 5, 15, 15, 15, 8, 8, 8, 8, 8, 8, 8, 5, 5] 113 rigid atoms, others: [3, 4, 5, 6, 12, 13, 14, 15] set([0, 1, 2, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 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: 115 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312655 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1C[C@@H](C(=O)OC)[C@H](C(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 1, 11, 12, 5, 5, 7, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 113 conformations in input total number of sets (complete confs): 113 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 16, 5, 5, 5, 5, 16, 23, 23, 23, 23, 5, 5, 1, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 1, 3, 3, 1, 29, 29, 29, 16, 16, 16, 16, 1, 1, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 1, 1] 113 rigid atoms, others: [48, 36, 37, 49, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 26, 27, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 205 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312655 none C#CCCN1C(CC2=NN=N[N-]2)=NN=C1N1C[C@@H](C(=O)OC)[C@H](C(C)C)C1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'O.3', '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: [1, 1, 5, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 7, 1, 11, 12, 5, 5, 7, 5, 5, 5, 5, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 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 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 21, 8, 8, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 24, 24, 24, 24, 52, 52, 52, 24, 24, 24, 26, 26, 24, 31, 31, 31, 21, 21, 4, 4, 24, 24, 52, 52, 52, 26, 26, 26, 26, 26, 26, 26, 24, 24] 112 rigid atoms, others: [6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 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: 259 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312655 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312655 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312655/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312655/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312655 Building REAL300020312656 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312656' /scratch/stefan/7770667/working/building/REAL300020312656 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312656 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312656/0 /scratch/stefan/7770667/working/building/REAL300020312656 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/255 `/scratch/stefan/7770667/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)C1=NN=C(CC2=NN=N[N-]2)N1CC1=CSC(N(C)C(C)=O)=N1) `REAL300020312656.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312656 none CCCN(C)C1=NN=C(CC2=NN=N[N-]2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 7, 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, 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] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 6, 20, 20, 20, 20, 77, 77, 92, 92, 20, 27, 27, 27, 27, 27, 16, 16, 4, 4, 4, 5, 5, 6, 6, 20, 77, 77, 77, 92, 92, 92] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 15, 16] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 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: 399 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312656 none CCCN(C)C1=NN=C(CC2=NN=N[N-]2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 7, 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, 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] 0 hydrogens 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, 81, 37, 20, 37, 20, 20, 20, 20, 20, 26, 37, 37, 37, 37, 9, 1, 1, 1, 1, 1, 1, 8, 8, 14, 14, 1, 97, 97, 97, 97, 97, 81, 81, 37, 37, 37, 26, 26, 9, 9, 1, 9, 9, 9, 14, 14, 14] 201 rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312656 none CCCN(C)C1=NN=C(CC2=NN=N[N-]2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 7, 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, 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] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [56, 45, 14, 6, 14, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 6, 6, 8, 30, 30, 30, 30, 107, 107, 125, 125, 30, 60, 60, 60, 60, 60, 45, 45, 14, 14, 14, 3, 3, 8, 8, 30, 107, 107, 107, 125, 125, 125] 191 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 586 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312656 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312656/1 /scratch/stefan/7770667/working/building/REAL300020312656 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/256 `/scratch/stefan/7770667/working/3D/256' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)C1=NN=C(CC2=N[N-]N=N2)N1CC1=CSC(N(C)C(C)=O)=N1) `REAL300020312656.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312656 none CCCN(C)C1=NN=C(CC2=N[N-]N=N2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 7, 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, 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] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 6, 20, 20, 20, 20, 77, 77, 93, 93, 20, 27, 27, 27, 27, 27, 16, 16, 4, 4, 4, 5, 5, 6, 6, 20, 77, 77, 77, 93, 93, 93] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 15, 16] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 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: 403 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312656 none CCCN(C)C1=NN=C(CC2=N[N-]N=N2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 7, 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, 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] 0 hydrogens 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, 81, 37, 20, 37, 20, 20, 20, 20, 20, 26, 37, 37, 37, 37, 9, 1, 1, 1, 1, 1, 1, 8, 8, 14, 14, 1, 98, 98, 98, 98, 98, 81, 81, 37, 37, 37, 26, 26, 9, 9, 1, 9, 9, 9, 14, 14, 14] 201 rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312656 none CCCN(C)C1=NN=C(CC2=N[N-]N=N2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 7, 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, 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] 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, 45, 14, 6, 14, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 6, 6, 8, 30, 30, 30, 30, 107, 107, 124, 124, 30, 60, 60, 60, 60, 60, 45, 45, 14, 14, 14, 3, 3, 8, 8, 30, 107, 107, 107, 124, 124, 124] 190 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 582 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312656 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312656 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312656/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312656/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312656 Building REAL300020312657 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312657' /scratch/stefan/7770667/working/building/REAL300020312657 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312657 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312657/0 /scratch/stefan/7770667/working/building/REAL300020312657 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/257 `/scratch/stefan/7770667/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)C1=NN=C(CC2=NN=N[N-]2)N1CC1=CSC(N(C)C(C)=O)=N1) `REAL300020312657.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312657 none CCCN(C)C1=NN=C(CC2=NN=N[N-]2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 7, 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, 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] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 6, 20, 20, 20, 20, 77, 77, 92, 92, 20, 27, 27, 27, 27, 27, 16, 16, 4, 4, 4, 5, 5, 6, 6, 20, 77, 77, 77, 92, 92, 92] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 15, 16] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 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: 399 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312657 none CCCN(C)C1=NN=C(CC2=NN=N[N-]2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 7, 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, 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] 0 hydrogens 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, 81, 37, 20, 37, 20, 20, 20, 20, 20, 26, 37, 37, 37, 37, 9, 1, 1, 1, 1, 1, 1, 8, 8, 14, 14, 1, 97, 97, 97, 97, 97, 81, 81, 37, 37, 37, 26, 26, 9, 9, 1, 9, 9, 9, 14, 14, 14] 201 rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312657 none CCCN(C)C1=NN=C(CC2=NN=N[N-]2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 7, 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, 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] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [56, 45, 14, 6, 14, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 6, 6, 8, 30, 30, 30, 30, 107, 107, 125, 125, 30, 60, 60, 60, 60, 60, 45, 45, 14, 14, 14, 3, 3, 8, 8, 30, 107, 107, 107, 125, 125, 125] 191 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 586 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312657 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312657/1 /scratch/stefan/7770667/working/building/REAL300020312657 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/258 `/scratch/stefan/7770667/working/3D/258' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)C1=NN=C(CC2=N[N-]N=N2)N1CC1=CSC(N(C)C(C)=O)=N1) `REAL300020312657.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312657 none CCCN(C)C1=NN=C(CC2=N[N-]N=N2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 7, 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, 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] 0 hydrogens 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, 4, 1, 4, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 6, 20, 20, 20, 20, 77, 77, 93, 93, 20, 27, 27, 27, 27, 27, 16, 16, 4, 4, 4, 5, 5, 6, 6, 20, 77, 77, 77, 93, 93, 93] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 15, 16] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 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: 403 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312657 none CCCN(C)C1=NN=C(CC2=N[N-]N=N2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 7, 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, 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] 0 hydrogens 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, 81, 37, 20, 37, 20, 20, 20, 20, 20, 26, 37, 37, 37, 37, 9, 1, 1, 1, 1, 1, 1, 8, 8, 14, 14, 1, 98, 98, 98, 98, 98, 81, 81, 37, 37, 37, 26, 26, 9, 9, 1, 9, 9, 9, 14, 14, 14] 201 rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312657 none CCCN(C)C1=NN=C(CC2=N[N-]N=N2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 7, 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, 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] 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, 45, 14, 6, 14, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 6, 6, 8, 30, 30, 30, 30, 107, 107, 124, 124, 30, 60, 60, 60, 60, 60, 45, 45, 14, 14, 14, 3, 3, 8, 8, 30, 107, 107, 107, 124, 124, 124] 190 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 582 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312657 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312657 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312657/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312657/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312657 Building REAL300020312658 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312658' /scratch/stefan/7770667/working/building/REAL300020312658 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312658 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312658/0 /scratch/stefan/7770667/working/building/REAL300020312658 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/259 `/scratch/stefan/7770667/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN(C)C1=NN=C(CC2=NN=N[N-]2)N1CC1=CSC(N(C)C(C)=O)=N1) `REAL300020312658.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312658/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312658 none C#CCN(C)C1=NN=C(CC2=NN=N[N-]2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.2', 'N.2', '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, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 7, 7, 7, 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, 7, 7, 7, 7, 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 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 5, 1, 5, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 6, 22, 22, 22, 22, 64, 64, 77, 77, 22, 20, 20, 20, 5, 5, 5, 5, 5, 6, 6, 22, 64, 64, 64, 77, 77, 77] 161 rigid atoms, others: [3, 5, 6, 7, 8, 9, 15, 16] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 17, 18, 19, 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: 285 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312658 none C#CCN(C)C1=NN=C(CC2=NN=N[N-]2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.2', 'N.2', '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, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 7, 7, 7, 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, 7, 7, 7, 7, 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 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 43, 22, 43, 22, 22, 22, 22, 22, 28, 40, 40, 40, 40, 9, 1, 1, 1, 1, 1, 1, 8, 8, 14, 14, 1, 96, 96, 96, 43, 43, 43, 28, 28, 9, 9, 1, 9, 9, 9, 14, 14, 14] 161 rigid atoms, others: [37, 16, 17, 18, 19, 20, 21, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 466 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312658 none C#CCN(C)C1=NN=C(CC2=NN=N[N-]2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.2', 'N.2', '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, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 7, 7, 7, 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, 7, 7, 7, 7, 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 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 17, 7, 17, 7, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 13, 40, 40, 40, 40, 97, 97, 106, 106, 40, 47, 47, 47, 17, 17, 17, 3, 3, 13, 13, 40, 97, 97, 97, 106, 106, 106] 161 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 423 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312658 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312658/1 /scratch/stefan/7770667/working/building/REAL300020312658 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/260 `/scratch/stefan/7770667/working/3D/260' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN(C)C1=NN=C(CC2=N[N-]N=N2)N1CC1=CSC(N(C)C(C)=O)=N1) `REAL300020312658.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312658/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312658 none C#CCN(C)C1=NN=C(CC2=N[N-]N=N2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.2', 'N.2', '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, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 7, 7, 7, 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, 7, 7, 7, 7, 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 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 5, 1, 5, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 6, 22, 22, 22, 22, 64, 64, 77, 77, 22, 20, 20, 20, 5, 5, 5, 5, 5, 6, 6, 22, 64, 64, 64, 77, 77, 77] 161 rigid atoms, others: [3, 5, 6, 7, 8, 9, 15, 16] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 17, 18, 19, 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: 285 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312658 none C#CCN(C)C1=NN=C(CC2=N[N-]N=N2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.2', 'N.2', '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, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 7, 7, 7, 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, 7, 7, 7, 7, 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 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 43, 22, 43, 22, 22, 22, 22, 22, 28, 40, 40, 40, 40, 9, 1, 1, 1, 1, 1, 1, 8, 8, 14, 14, 1, 96, 96, 96, 43, 43, 43, 28, 28, 9, 9, 1, 9, 9, 9, 14, 14, 14] 161 rigid atoms, others: [37, 16, 17, 18, 19, 20, 21, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 466 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312658 none C#CCN(C)C1=NN=C(CC2=N[N-]N=N2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.2', 'N.2', '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, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 7, 7, 7, 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, 7, 7, 7, 7, 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 161 conformations in input total number of sets (complete confs): 161 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 17, 7, 17, 7, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 13, 40, 40, 40, 40, 97, 97, 106, 106, 40, 47, 47, 47, 17, 17, 17, 3, 3, 13, 13, 40, 97, 97, 97, 106, 106, 106] 161 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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: 423 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312658 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312658 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312658/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312658/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312658 Building REAL300020312659 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312659' /scratch/stefan/7770667/working/building/REAL300020312659 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312659 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312659/0 /scratch/stefan/7770667/working/building/REAL300020312659 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/261 `/scratch/stefan/7770667/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCN(C)C1=NN=C(CC2=NN=N[N-]2)N1CC1=CSC(N(C)C(C)=O)=N1) `REAL300020312659.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312659 none C=CCN(C)C1=NN=C(CC2=NN=N[N-]2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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: [1, 1, 5, 8, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 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, 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] 0 hydrogens 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, 19, 5, 1, 5, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 1, 1, 6, 22, 22, 22, 22, 69, 69, 83, 83, 22, 42, 42, 42, 19, 19, 5, 5, 5, 3, 3, 6, 6, 22, 69, 69, 69, 83, 83, 83] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 15, 16] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312659 none C=CCN(C)C1=NN=C(CC2=NN=N[N-]2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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: [1, 1, 5, 8, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 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, 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] 0 hydrogens 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, 105, 42, 22, 42, 22, 22, 22, 22, 22, 22, 35, 35, 35, 35, 9, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 1, 148, 148, 148, 105, 105, 42, 42, 42, 22, 22, 9, 9, 1, 7, 7, 7, 11, 11, 11] 201 rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312659 none C=CCN(C)C1=NN=C(CC2=NN=N[N-]2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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: [1, 1, 5, 8, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 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, 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] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [87, 53, 16, 5, 16, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 5, 5, 7, 30, 30, 30, 30, 70, 70, 77, 77, 30, 87, 87, 87, 53, 53, 16, 16, 16, 3, 3, 7, 7, 30, 70, 70, 70, 77, 77, 77] 168 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 493 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312659 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312659/1 /scratch/stefan/7770667/working/building/REAL300020312659 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/262 `/scratch/stefan/7770667/working/3D/262' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCN(C)C1=NN=C(CC2=N[N-]N=N2)N1CC1=CSC(N(C)C(C)=O)=N1) `REAL300020312659.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312659/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312659 none C=CCN(C)C1=NN=C(CC2=N[N-]N=N2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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: [1, 1, 5, 8, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 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, 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] 0 hydrogens 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, 19, 5, 1, 5, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 1, 1, 6, 22, 22, 22, 22, 69, 69, 83, 83, 22, 42, 42, 42, 19, 19, 5, 5, 5, 3, 3, 6, 6, 22, 69, 69, 69, 83, 83, 83] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 15, 16] set([0, 1, 2, 4, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312659 none C=CCN(C)C1=NN=C(CC2=N[N-]N=N2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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: [1, 1, 5, 8, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 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, 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] 0 hydrogens 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, 105, 42, 22, 42, 22, 22, 22, 22, 22, 22, 35, 35, 35, 35, 9, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 1, 148, 148, 148, 105, 105, 42, 42, 42, 22, 22, 9, 9, 1, 7, 7, 7, 11, 11, 11] 201 rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312659 none C=CCN(C)C1=NN=C(CC2=N[N-]N=N2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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: [1, 1, 5, 8, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 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, 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] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [87, 53, 16, 5, 16, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 5, 5, 7, 30, 30, 30, 30, 70, 70, 77, 77, 30, 87, 87, 87, 53, 53, 16, 16, 16, 3, 3, 7, 7, 30, 70, 70, 70, 77, 77, 77] 167 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 493 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312659 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312659 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312659/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312659/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312659 Building REAL300020312660 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312660' /scratch/stefan/7770667/working/building/REAL300020312660 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312660 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312660/0 /scratch/stefan/7770667/working/building/REAL300020312660 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/263 `/scratch/stefan/7770667/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)C1=NC(CN2C(CC3=NN=N[N-]3)=NN=C2N2CCCC2)=CS1) `REAL300020312660.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312660 none CC(=O)N(C)C1=NC(CN2C(CC3=NN=N[N-]3)=NN=C2N2CCCC2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', '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, 11, 8, 5, 1, 8, 1, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 10, 14, 10, 10, 6, 4, 4, 4, 4, 6, 6, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 10, 10, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 10] 14 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 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, 45]) total number of confs: 52 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312660 none CC(=O)N(C)C1=NC(CN2C(CC3=NN=N[N-]3)=NN=C2N2CCCC2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', '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, 11, 8, 5, 1, 8, 1, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 3, 1, 1, 1, 1, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 3, 3, 3, 3, 3, 3, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1] 14 rigid atoms, others: [3, 5, 6, 7, 8, 45, 25, 26] set([0, 1, 2, 4, 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]) total number of confs: 34 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312660 none CC(=O)N(C)C1=NC(CN2C(CC3=NN=N[N-]3)=NN=C2N2CCCC2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', '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, 11, 8, 5, 1, 8, 1, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 10, 14, 10, 10, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 6, 10, 10, 14, 14, 14, 14, 14, 14, 5, 5, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 10] 14 rigid atoms, others: [11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 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: 38 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312660 none CC(=O)N(C)C1=NC(CN2C(CC3=NN=N[N-]3)=NN=C2N2CCCC2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', '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, 11, 8, 5, 1, 8, 1, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 10, 14, 10, 10, 5, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 4, 10, 10, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 10] 14 rigid atoms, others: [8, 9, 10, 11, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 21, 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: 60 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312660 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312660/1 /scratch/stefan/7770667/working/building/REAL300020312660 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/264 `/scratch/stefan/7770667/working/3D/264' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)C1=NC(CN2C(CC3=N[N-]N=N3)=NN=C2N2CCCC2)=CS1) `REAL300020312660.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312660 none CC(=O)N(C)C1=NC(CN2C(CC3=N[N-]N=N3)=NN=C2N2CCCC2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', '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, 11, 8, 5, 1, 8, 1, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 10, 14, 10, 10, 6, 4, 4, 4, 4, 6, 6, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 10, 10, 14, 14, 14, 14, 14, 14, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 10] 14 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 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, 45]) total number of confs: 52 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312660 none CC(=O)N(C)C1=NC(CN2C(CC3=N[N-]N=N3)=NN=C2N2CCCC2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', '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, 11, 8, 5, 1, 8, 1, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 3, 1, 1, 1, 1, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 3, 3, 3, 3, 3, 3, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1] 14 rigid atoms, others: [3, 5, 6, 7, 8, 45, 25, 26] set([0, 1, 2, 4, 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]) total number of confs: 34 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312660 none CC(=O)N(C)C1=NC(CN2C(CC3=N[N-]N=N3)=NN=C2N2CCCC2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', '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, 11, 8, 5, 1, 8, 1, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 10, 14, 10, 10, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 6, 6, 6, 6, 10, 10, 14, 14, 14, 14, 14, 14, 5, 5, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 10] 14 rigid atoms, others: [11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 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: 38 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312660 none CC(=O)N(C)C1=NC(CN2C(CC3=N[N-]N=N3)=NN=C2N2CCCC2)=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', '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, 11, 8, 5, 1, 8, 1, 5, 8, 1, 5, 1, 8, 8, 8, 8, 8, 8, 1, 8, 5, 5, 5, 5, 1, 14, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 10, 14, 10, 10, 5, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 4, 10, 10, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 10] 14 rigid atoms, others: [8, 9, 10, 11, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 12, 13, 14, 15, 16, 21, 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: 60 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312660 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312660 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312660/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312660/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312660 Building REAL300020312661 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312661' /scratch/stefan/7770667/working/building/REAL300020312661 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312661 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312661/0 /scratch/stefan/7770667/working/building/REAL300020312661 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/265 `/scratch/stefan/7770667/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON(C)C1=NN=C(CCC2=N[N-]N=N2)N1CC1=CSC(N(C)C(C)=O)=N1) `REAL300020312661.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312661 none CON(C)C1=NN=C(CCC2=N[N-]N=N2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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, 12, 8, 5, 1, 8, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 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, 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] 0 hydrogens 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, 6, 1, 1, 1, 1, 1, 6, 10, 16, 16, 16, 16, 1, 1, 5, 21, 21, 21, 21, 60, 60, 77, 77, 21, 12, 12, 12, 6, 6, 6, 5, 5, 10, 10, 5, 5, 21, 60, 60, 60, 77, 77, 77] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 15, 16] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312661 none CON(C)C1=NN=C(CCC2=N[N-]N=N2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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, 12, 8, 5, 1, 8, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 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, 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] 0 hydrogens 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, 46, 21, 46, 21, 21, 21, 21, 21, 61, 74, 107, 107, 107, 107, 9, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 1, 63, 63, 63, 46, 46, 46, 61, 61, 74, 74, 9, 9, 1, 7, 7, 7, 12, 12, 12] 201 rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312661 none CON(C)C1=NN=C(CCC2=N[N-]N=N2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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, 12, 8, 5, 1, 8, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 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, 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] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [58, 48, 18, 48, 17, 17, 17, 7, 4, 1, 1, 1, 1, 1, 1, 18, 18, 34, 99, 99, 99, 99, 151, 151, 153, 153, 99, 58, 58, 58, 48, 48, 48, 7, 7, 4, 4, 34, 34, 99, 151, 151, 151, 153, 153, 153] 164 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 503 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312661 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312661/1 /scratch/stefan/7770667/working/building/REAL300020312661 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/266 `/scratch/stefan/7770667/working/3D/266' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON(C)C1=NN=C(CCC2=NN=N[N-]2)N1CC1=CSC(N(C)C(C)=O)=N1) `REAL300020312661.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312661 none CON(C)C1=NN=C(CCC2=NN=N[N-]2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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, 12, 8, 5, 1, 8, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 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, 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] 0 hydrogens 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, 6, 1, 1, 1, 1, 1, 6, 10, 16, 16, 16, 16, 1, 1, 5, 21, 21, 21, 21, 60, 60, 77, 77, 21, 12, 12, 12, 6, 6, 6, 5, 5, 10, 10, 5, 5, 21, 60, 60, 60, 77, 77, 77] 201 rigid atoms, others: [2, 4, 5, 6, 7, 8, 15, 16] set([0, 1, 3, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312661 none CON(C)C1=NN=C(CCC2=NN=N[N-]2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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, 12, 8, 5, 1, 8, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 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, 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] 0 hydrogens 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, 46, 21, 46, 21, 21, 21, 21, 21, 61, 74, 107, 107, 107, 107, 9, 1, 1, 1, 1, 1, 1, 6, 6, 12, 12, 1, 63, 63, 63, 46, 46, 46, 61, 61, 74, 74, 9, 9, 1, 7, 7, 7, 12, 12, 12] 201 rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45]) 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312661 none CON(C)C1=NN=C(CCC2=NN=N[N-]2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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, 12, 8, 5, 1, 8, 8, 1, 5, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 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, 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] 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: [59, 49, 19, 49, 18, 18, 18, 8, 4, 1, 1, 1, 1, 1, 1, 18, 19, 35, 100, 100, 100, 100, 152, 152, 154, 154, 100, 59, 59, 59, 49, 49, 49, 8, 8, 4, 4, 35, 35, 100, 152, 152, 152, 154, 154, 154] 165 rigid atoms, others: [9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 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]) total number of confs: 509 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312661 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312661 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312661/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312661/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312661 Building REAL300020312662 mkdir: created directory `/scratch/stefan/7770667/working/building/REAL300020312662' /scratch/stefan/7770667/working/building/REAL300020312662 /scratch/stefan/7770667/working /scratch/stefan/7770667 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300020312662 mkdir: created directory `0' /scratch/stefan/7770667/working/building/REAL300020312662/0 /scratch/stefan/7770667/working/building/REAL300020312662 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/267 `/scratch/stefan/7770667/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON(C)C1=NN=C(CC2=NN=N[N-]2)N1CC1=CSC(N(C)C(C)=O)=N1) `REAL300020312662.mol2' -> `0.mol2' `temp.mol2' -> `REAL300020312662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312662 none CON(C)C1=NN=C(CC2=NN=N[N-]2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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, 12, 8, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 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, 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 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [12, 8, 1, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 4, 12, 12, 12, 12, 46, 46, 52, 52, 12, 12, 12, 12, 8, 8, 8, 5, 5, 4, 4, 12, 46, 46, 46, 52, 52, 52] 87 rigid atoms, others: [2, 4, 5, 6, 7, 8, 14, 15] set([0, 1, 3, 9, 10, 11, 12, 13, 16, 17, 18, 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: 174 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312662 none CON(C)C1=NN=C(CC2=NN=N[N-]2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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, 12, 8, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 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, 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 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 12, 19, 12, 12, 12, 12, 12, 16, 23, 23, 23, 23, 8, 1, 1, 1, 1, 1, 1, 7, 7, 11, 11, 1, 28, 28, 28, 19, 19, 19, 16, 16, 8, 8, 1, 8, 8, 8, 11, 11, 11] 87 rigid atoms, others: [36, 15, 16, 17, 18, 19, 20, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 145 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312662 none CON(C)C1=NN=C(CC2=NN=N[N-]2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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, 12, 8, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 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, 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 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [25, 18, 7, 18, 7, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 10, 23, 23, 23, 23, 72, 72, 79, 79, 23, 25, 25, 25, 18, 18, 18, 3, 3, 10, 10, 23, 72, 72, 72, 79, 79, 79] 87 rigid atoms, others: [8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 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]) total number of confs: 251 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312662 /scratch/stefan/7770667/working /scratch/stefan/7770667 mkdir: created directory `1' /scratch/stefan/7770667/working/building/REAL300020312662/1 /scratch/stefan/7770667/working/building/REAL300020312662 /scratch/stefan/7770667/working /scratch/stefan/7770667 Protomer 1 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7770667/working/3D/268 `/scratch/stefan/7770667/working/3D/268' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON(C)C1=NN=C(CC2=N[N-]N=N2)N1CC1=CSC(N(C)C(C)=O)=N1) `REAL300020312662.mol2' -> `1.mol2' `temp.mol2' -> `REAL300020312662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7770667/working/building/REAL300020312662/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window 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.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312662 none CON(C)C1=NN=C(CC2=N[N-]N=N2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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, 12, 8, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 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, 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 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [12, 8, 1, 8, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 4, 12, 12, 12, 12, 46, 46, 52, 52, 12, 12, 12, 12, 8, 8, 8, 5, 5, 4, 4, 12, 46, 46, 46, 52, 52, 52] 87 rigid atoms, others: [2, 4, 5, 6, 7, 8, 14, 15] set([0, 1, 3, 9, 10, 11, 12, 13, 16, 17, 18, 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: 174 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312662 none CON(C)C1=NN=C(CC2=N[N-]N=N2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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, 12, 8, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 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, 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 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [28, 19, 12, 19, 12, 12, 12, 12, 12, 16, 23, 23, 23, 23, 8, 1, 1, 1, 1, 1, 1, 7, 7, 11, 11, 1, 28, 28, 28, 19, 19, 19, 16, 16, 8, 8, 1, 8, 8, 8, 11, 11, 11] 87 rigid atoms, others: [36, 15, 16, 17, 18, 19, 20, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 145 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.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300020312662 none CON(C)C1=NN=C(CC2=N[N-]N=N2)N1CC1=CSC(N(C)C(C)=O)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.pl3', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'N.2', 'N.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.3', 'C.2', 'C.3', 'O.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, 12, 8, 5, 1, 8, 8, 1, 5, 1, 8, 8, 8, 8, 8, 5, 1, 1, 14, 1, 8, 5, 1, 5, 11, 8, 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, 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 87 conformations in input total number of sets (complete confs): 87 using faster count positions algorithm for large data unique positions, atoms: [25, 18, 7, 18, 7, 7, 7, 3, 1, 1, 1, 1, 1, 1, 7, 7, 10, 23, 23, 23, 23, 72, 72, 79, 79, 23, 25, 25, 25, 18, 18, 18, 3, 3, 10, 10, 23, 72, 72, 72, 79, 79, 79] 87 rigid atoms, others: [8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 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]) total number of confs: 251 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7770667/working/building/REAL300020312662 /scratch/stefan/7770667/working /scratch/stefan/7770667 Finished preparing REAL300020312662 Recording results /scratch/stefan/7770667/working /scratch/stefan/7770667 Appending to /scratch/stefan/7770667/finished/xaaaagz.* 0: /scratch/stefan/7770667/working/building/REAL300020312662/0.* 1: /scratch/stefan/7770667/working/building/REAL300020312662/1.* Removing working files in /scratch/stefan/7770667/working/building/REAL300020312662 /scratch/stefan/7770667 Compressing combined databse files /scratch/stefan/7770667/finished/xaaaagz.db2.gz /scratch/stefan/7770667/finished/xaaaagz.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7770667/finished) ======================================================= Finalizing... removed `/scratch/stefan/7770667/working/3D/269' removed `/scratch/stefan/7770667/working/3D/190' removed directory: `/scratch/stefan/7770667/working/3D' `/scratch/stefan/7770667/working/protonate' -> `/scratch/stefan/7770667/archive' `/scratch/stefan/7770667/working/input-smiles.ism' -> `/scratch/stefan/7770667/archive/input-smiles.ism' rmdir: removing directory, `/scratch/stefan/7770667/working/building' rmdir: removing directory, `/scratch/stefan/7770667/working' ls: No match. ls: No match.